From ad95e4f03ea5c5f7ee4a7eca1b001a45666f637c Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Tue, 7 May 2013 23:26:55 +0000
Subject: Made some progress adding species/group tabs to the quick search
 result page to make the results easier to navigate

---
 wqflask/wqflask/search_results.py           |  21 +-
 wqflask/wqflask/templates/quick_search.html | 323 +++++++++++++++++++---------
 2 files changed, 235 insertions(+), 109 deletions(-)

diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 89f146b3..5f3c036f 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -74,6 +74,7 @@ class SearchResultPage(object):
             self.search_terms = kw['q']
             print("self.search_terms is: ", self.search_terms)
             self.quick_search()
+            self.get_group_species_tree()
         else:
             self.results = []
             #self.quick_search = False
@@ -134,16 +135,32 @@ class SearchResultPage(object):
         type_dict = {'PublishXRef': 'phenotype',
                    'ProbeSetXRef': 'mrna_assay',
                    'GenoXRef': 'genotype'}
-
+        
+        self.species_groups = {}
         for dbresult in dbresults:
             this_result = {}
             this_result['table_name'] = dbresult.table_name
             this_result['key'] = dbresult.the_key
             this_result['result_fields'] = json.loads(dbresult.result_fields)
-            
+            this_species = this_result['result_fields']['species']
+            this_group = this_result['result_fields']['group_name']
+            if type_dict[dbresult.table_name] not in self.species_groups:
+                self.species_groups[type_dict[dbresult.table_name]] = {}
+            if this_species not in self.species_groups[type_dict[dbresult.table_name]]:
+                self.species_groups[type_dict[dbresult.table_name]][this_species] = collections.defaultdict(list)
+            if this_group not in self.species_groups[type_dict[dbresult.table_name]][this_species]:
+                self.species_groups[type_dict[dbresult.table_name]][this_species].append(this_group)
             self.results[type_dict[dbresult.table_name]].append(this_result)
             
         #print("results: ", pf(self.results['phenotype']))
+        
+    #def get_group_species_tree(self):
+    #    self.species_groups = collections.default_dict(list)
+    #    for key in self.results:
+    #        for item in self.results[key]:
+    #            self.species_groups[item['result_fields']['species']].append(
+    #                                        item['result_fields']['group_name'])
+
 
     #def quick_search(self):
     #    self.search_terms = parser.parse(self.search_terms)
diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html
index 769c40e6..9d5b0c74 100644
--- a/wqflask/wqflask/templates/quick_search.html
+++ b/wqflask/wqflask/templates/quick_search.html
@@ -21,9 +21,7 @@
         <ul>
             {% if search_terms %}
             <li>
-                {% for word in search_terms %}
-                    <strong>{{word}}</strong> {% if not loop.last %} or {% endif %}
-                {% endfor %}
+                <strong>{{search_terms}}</strong> 
             </li>
             {% endif %}
         </ul>
@@ -33,20 +31,166 @@
 
         <div class="tabbable"> <!-- Only required for left/right tabs -->
             <ul class="nav nav-tabs">
+                {% if results.phenotype %}
                 <li class="active"> <a href="#tab1" data-toggle="tab">Phenotype</a></li>
+                {% endif %}
+                {% if results.mrna_assay %}
                 <li>                <a href="#tab2" data-toggle="tab">mRNA Assay</a></li>
+                {% endif %}
+                {% if results.genotype %}
                 <li>                <a href="#tab3" data-toggle="tab">Genotype</a></li>
+                {% endif %}
             </ul>
             <div class="tab-content">
                 <div class="tab-pane active" id="tab1">
-                    <table class="table table-hover">
+                    <div class="tabbable tabs-left">
+                        <ul class="nav nav-tabs">
+                            {% for species in species_groups.phenotype %}
+                            <li> <a href="#tab1_{{ loop.index }}" data-toggle="tab">{{ species }}</a></li>
+                            {% endfor %}
+                        </ul>
+                        <div class="tab-content">
+                            {% for species in species_groups.phenotype %}
+                            <div class="tab-pane active" id="tab{{ loop.index }}">
+                                <table id="pheno_results" class="table table-hover table-striped table-bordered">
+                                    <thead>
+                                        <tr>
+                                        <th>Id</th>
+                                        <th>Species</th>
+                                        <th>Group</th>
+                                        <th>Description</th>
+                                        <th>LRS</th>
+                                        <th>Year</th>
+                                        <th>Authors</th>
+                                        </tr>
+                                    </thead>
+                                    <tbody>
+                                        {% for result in results.phenotype %}
+                                        {% if result.result_fields['species'] == species %}
+                                        <tr>
+                                            <td>{{ result.result_fields['phenotype_id'] }}</td>
+                                            <td>{{ result.result_fields['species'] }}</td>
+                                            <td>{{ result.result_fields['group_name'] }}</td>
+                                            <td>{{ result.result_fields['description'] }}</td>
+                                            <td>{{ result.result_fields['lrs'] }}</td>
+                                            <td>
+                                                <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ result.result_fields['pubmed_id'] }}&dopt=Abstract">
+                                                    {{ result.result_fields['year'] }}
+                                                </a>
+                                            </td>
+                                            <td>{{ result.result_fields['authors'] }}</td>
+                                        </tr>
+                                        {% endif %}
+                                        {% endfor %}
+                                    </tbody>
+                                </table>
+                            </div>
+                            {% endfor %}
+                        </div>
+                    </div>
+                </div>
+                <div class="tab-pane active" id="tab2">
+                    <div class="tabbable tabs-left">
+                        <ul class="nav nav-tabs">
+                            {% for species in species_groups.mrna_assay %}
+                            <li> <a href="#tab2_{{ loop.index }}" data-toggle="tab">{{ species }}</a></li>
+                            {% endfor %}
+                        </ul>
+                        <div class="tab-content">
+                            {% for species in species_groups.mrna_assay %}
+                            <div class="tab-pane active" id="tab{{ loop.index }}">
+                                <table id="mrna_assay_results" class="table table-hover table-striped table-bordered">
+                                    <thead>
+                                        <tr>
+                                        <th>Record ID</th>
+                                        <th>Species</th>
+                                        <th>Group</th>
+                                        <th>Data Set</th>
+                                        <th>Symbol</th>
+                                        <th>Description</th>
+                                        <th>Location</th>
+                                        <th>Mean Expr</th>
+                                        <th>Max LRS</th>
+                                        </tr>
+                                    </thead>
+                                    <tbody>
+                                        {% for result in results.mrna_assay %}
+                                        {% if result.result_fields['species'] == species %}
+                                        <tr>
+                                            <td>
+                                                <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}"
+                                                   {{ result.result_fields['name'] }}
+                                                </a>
+                                            </td>
+                                            <td>{{ result.result_fields['species'] }}</td>
+                                            <td>{{ result.result_fields['group_name'] }}</td>
+                                            <td>{{ result.result_fields['dataset_name'] }}</td>
+                                            <td>{{ result.result_fields['symbol'] }}</td>
+                                            <td>{{ result.result_fields['description'] }}</td>
+                                            <td>{{ result.result_fields['chr'] }} : {{ result['mb'] }}</td>
+                                            <td>{{ result.result_fields['mean'] }}</td>
+                                            <td>{{ result.result_fields['lrs'] }}</td>
+                                        </tr>
+                                        {% endif %}
+                                        {% endfor %}
+                                    </tbody>
+                                </table>       
+                            </div>
+                            {% endfor %}
+                        </div>
+                    </div>
+                </div>
+                <div class="tab-pane active" id="tab3">
+                    <div class="tabbable tabs-left">
+                        <ul class="nav nav-tabs">
+                            {% for species in species_groups.genotype %}
+                            <li> <a href="#tab3_{{ loop.index }}" data-toggle="tab">{{ species }}</a></li>
+                            {% endfor %}
+                        </ul>
+                        <div class="tab-content">
+                            {% for species in species_groups.genotype %}
+                            <div class="tab-pane active" id="tab{{ loop.index }}">
+                                <table id="geno_results" class="table table-hover table-striped table-bordered">
+                                    <thead>
+                                        <tr>
+                                        <th>Marker</th>
+                                        <th>Species</th>
+                                        <th>Group</th>
+                                        <th>Data Set</th>
+                                        <th>Location</th>
+                                        </tr>
+                                    </thead>
+                                    <tbody>
+                                        {% for result in results.genotype %}
+                                        {% if result.result_fields['species'] == species %}
+                                        <tr>
+                                            <td>
+                                                <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['marker_name'] }}&dataset={{ result.result_fields['dataset'] }}">
+                                                    {{ result.result_fields['marker_name'] }}
+                                                </a>
+                                            </td>
+                                            <td>{{ result.result_fields['species'] }}</td>
+                                            <td>{{ result.result_fields['group_name'] }}</td>
+                                            <td>{{ result.result_fields['dataset_name'] }}</td>
+                                            <td>{{ result.result_fields['chr'] }} : {{ result.result_fields['mb'] }}</td>
+                                        </tr>
+                                        {% endif %}
+                                        {% endfor %}
+                                    </tbody>
+                                </table>   
+                            </div>
+                            {% endfor %}
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </div>
+    </div>
+    
+                {#
+                    <table id="pheno_results" class="table table-hover table-striped table-bordered">
                         <thead>
                             <tr>
-                        {#
-                            {% for key, _value in results.phenotype[0].result_fields.items() %}
-                                <th>{{key}}</th>
-                            {% endfor %}
-                        #}
                             <th>Id</th>
                             <th>Species</th>
                             <th>Group</th>
@@ -59,26 +203,24 @@
                         <tbody>
                             {% for result in results.phenotype %}
                             <tr>
-                                {% for result in result.result_fields.items() %}
-                                <td>{{ result['phenotype_id'] }}</td>
-                                <td>{{ result['species'] }}</td>
-                                <td>{{ result['group_name'] }}</td>
-                                <td>{{ result['description'] }}</td>
-                                <td>{{ result['lrs'] }}</td>
+                                <td>{{ result.result_fields['phenotype_id'] }}</td>
+                                <td>{{ result.result_fields['species'] }}</td>
+                                <td>{{ result.result_fields['group_name'] }}</td>
+                                <td>{{ result.result_fields['description'] }}</td>
+                                <td>{{ result.result_fields['lrs'] }}</td>
                                 <td>
-                                    <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ result['pubmed_id'] }}&dopt=Abstract">
-                                        {{ result['year'] }}
+                                    <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ result.result_fields['pubmed_id'] }}&dopt=Abstract">
+                                        {{ result.result_fields['year'] }}
                                     </a>
                                 </td>
-                                <td>{{ result['authors'] }}</td>
-                                {% endfor %}
+                                <td>{{ result.result_fields['authors'] }}</td>
                             </tr>
                             {% endfor %}
                         </tbody>
                     </table>
                 </div>
                 <div class="tab-pane" id="tab2">
-                    <table class="table table-hover">
+                    <table id="mrna_assay_results" class="table table-hover table-striped table-bordered">
                         <thead>
                             <tr>
                             <th>Record ID</th>
@@ -95,28 +237,26 @@
                         <tbody>
                             {% for result in results.mrna_assay %}
                             <tr>
-                                {% for result in result.result_fields.items() %}
                                 <td>
-                                    <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result['name'] }}&dataset={{ result['dataset'] }}"
-                                       {{ result['name'] }}
+                                    <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}"
+                                       {{ result.result_fields['name'] }}
                                     </a>
                                 </td>
-                                <td>{{ result['species'] }}</td>
-                                <td>{{ result['group_name'] }}</td>
-                                <td>{{ result['dataset_name'] }}</td>
-                                <td>{{ result['symbol'] }}</td>
-                                <td>{{ result['description'] }}</td>
-                                <td>{{ result['chr'] }} : {{ result['mb'] }}</td>
-                                <td>{{ result['mean'] }}</td>
-                                <td>{{ result['lrs'] }}</td>
-                                {% endfor %}
+                                <td>{{ result.result_fields['species'] }}</td>
+                                <td>{{ result.result_fields['group_name'] }}</td>
+                                <td>{{ result.result_fields['dataset_name'] }}</td>
+                                <td>{{ result.result_fields['symbol'] }}</td>
+                                <td>{{ result.result_fields['description'] }}</td>
+                                <td>{{ result.result_fields['chr'] }} : {{ result['mb'] }}</td>
+                                <td>{{ result.result_fields['mean'] }}</td>
+                                <td>{{ result.result_fields['lrs'] }}</td>
                             </tr>
                             {% endfor %}
                         </tbody>
                     </table>                    
                 </div>
                 <div class="tab-pane" id="tab3">
-                    <table class="table table-hover">
+                    <table id="geno_results" class="table table-hover table-striped table-bordered">
                         <thead>
                             <tr>
                             <th>Marker</th>
@@ -127,91 +267,60 @@
                             </tr>
                         </thead>
                         <tbody>
-                            {% for result in results.mrna_assay %}
+                            {% for result in results.genotype %}
                             <tr>
-                                {% for result in result.result_fields.items() %}
                                 <td>
-                                    <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result['marker_name'] }}&dataset={{ result['dataset'] }}">
-                                        {{ result['marker_name'] }}
+                                    <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['marker_name'] }}&dataset={{ result.result_fields['dataset'] }}">
+                                        {{ result.result_fields['marker_name'] }}
                                     </a>
                                 </td>
-                                <td>{{ result['species'] }}</td>
-                                <td>{{ result['group_name'] }}</td>
-                                <td>{{ result['dataset_name'] }}</td>
-                                <td>{{ result['chr'] }} : {{ result['mb'] }}</td>
-                                {% endfor %}
+                                <td>{{ result.result_fields['species'] }}</td>
+                                <td>{{ result.result_fields['group_name'] }}</td>
+                                <td>{{ result.result_fields['dataset_name'] }}</td>
+                                <td>{{ result.result_fields['chr'] }} : {{ result.result_fields['mb'] }}</td>
                             </tr>
                             {% endfor %}
                         </tbody>
                     </table>                     
                 </div>
-            </div>
-        </div>
-        
-        
-
-        <!--<div class="bs-docs-example">
-            <table class="table table-hover">
-                <thead>
-                    <tr>
-                    {% for header in header_fields %}
-                        <th>{{header}}</th>
-                    {% endfor %}
-                    </tr>
-                </thead>
-
-                <tbody>
-                    {% for this_trait in trait_list %}
-                    <TR id="{{ this_trait }}">
-                        <TD>
-                            <INPUT TYPE="checkbox" NAME="searchResult" class="checkbox"
-                                   VALUE="{{ this_trait }}">
-                        </TD>
-                        <TD>
-                            <a href="{{ url_for('show_trait_page',
-                                    trait_id = this_trait.name,
-                                    dataset = dataset.name
-                                    )}}">
-                                {{ this_trait.name }}
-                            </a>
-                        </TD>
-                        {% if dataset.type == 'ProbeSet' %}
-                            <TD>{{ this_trait.symbol }}</TD>
-                            <TD>{{ this_trait.description_display }}</TD>
-                            <TD>{{ this_trait.location_repr }}</TD>
-                            <TD>{{ this_trait.mean }}</TD>
-                            <TD>{{ this_trait.LRS_score_repr }}</TD>
-                            <TD>{{ this_trait.LRS_location_repr }}</TD>
-                        {% elif dataset.type == 'Publish' %}
-                            <TD>{{ this_trait.description_display }}</TD>
-                            <TD>{{ this_trait.authors }}</TD>
-                            <TD>
-                                <a href="{{ this_trait.pubmed_link }}">
-                                    {{ this_trait.pubmed_text }}
-                                </a>
-                            </TD>
-                            <TD>{{ this_trait.LRS_score_repr }}</TD>
-                            <TD>{{ this_trait.LRS_location_repr }}</TD>
-                        {% elif dataset.type == 'Geno' %}
-                            <TD>{{ this_trait.location_repr }}</TD>
-                        {% endif %}
-                    </TR>
-                {% endfor %}
-                </tbody>
+                #}
 
-            </table>
-
-            <br />
-
-            <button class="btn"><i class="icon-ok"></i> Select</button>
-            <button class="btn"><i class="icon-remove"></i> Deselect</button>
-            <button class="btn"><i class="icon-resize-vertical"></i> Invert</button>
-            <button class="btn"><i class="icon-plus-sign"></i> Add</button>
-            <button class="btn btn-primary pull-right"><i class="icon-download icon-white"></i> Download Table</button>
-        </div>-->
+<!-- End of body -->
 
-    </div>
+{% endblock %}
 
-<!-- End of body -->
+{% block js %}  
+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
 
+    
+    <script type="text/javascript" charset="utf-8">
+        $(document).ready( function () {
+            console.time("Creating table");
+            $('#pheno_results, #mrna_assay_results, #geno_results').dataTable( {
+                //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
+                "sDom": "lTftipr",
+                "oTableTools": {
+                    "aButtons": [
+                        "copy",
+                        "print",
+                        {
+                            "sExtends":    "collection",
+                            "sButtonText": 'Save <span class="caret" />',
+                            "aButtons":    [ "csv", "xls", "pdf" ]
+                        }
+                    ],
+                    "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
+                },
+                "iDisplayLength": 50,
+                "bLengthChange": true,
+                "bDeferRender": true,
+                "bSortClasses": false
+            } );
+            console.timeEnd("Creating table");
+        });
+    </script>
 {% endblock %}
-- 
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