From e67129ad901bb2af29f4f00ba5d4d5b9b94ae705 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 25 Oct 2016 16:39:47 +0000
Subject: Replaced the Download Table button for collection page with python
 version that displays metadata, etc

Removed currently unused javascript and css imports related to the DataTables buttons import (since it was replaced with the python export) from regular search, both global searches, and the view_collection page

Added a bunch of parameters to the jsonable function for the GeneralTrait object in order to later create a json version of the search results and implement the client-side Scroller feature (which dynamically loads table rows from json when you scroll)
---
 wqflask/base/trait.py                             | 34 +++++++++++--
 wqflask/wqflask/templates/collections/view.html   | 59 ++++++++++-------------
 wqflask/wqflask/templates/gsearch_gene.html       |  4 --
 wqflask/wqflask/templates/gsearch_pheno.html      |  4 --
 wqflask/wqflask/templates/search_result_page.html |  4 --
 5 files changed, 55 insertions(+), 50 deletions(-)

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 32032ba7..358138f5 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -78,10 +78,36 @@ class GeneralTrait(object):
         """Return a dict suitable for using as json
 
         Actual turning into json doesn't happen here though"""
-        return dict(name=self.name,
-                    dataset=self.dataset.name,
-                    description=self.description_display,
-                    mean=self.mean)
+        
+        if self.dataset.type == "ProbeSet":
+            return dict(name=self.name,
+                        symbol=self.symbol,
+                        dataset=self.dataset.name,
+                        description=self.description_display,
+                        mean=self.mean,
+                        location=self.location_repr,
+                        lrs_score=self.LRS_score_repr,
+                        lrs_location=self.LRS_location_repr,
+                        additive=self.additive
+                        )
+        elif self.dataset.type == "Publish":
+            return dict(name=self.name,
+                        dataset=self.dataset.name,
+                        description=self.description_display,
+                        authors=self.authors,
+                        pubmed_text=self.pubmed_text,
+                        pubmed_link=self.pubmed_link,
+                        lrs_score=self.LRS_score_repr,
+                        lrs_location=self.LRS_location_repr,
+                        additive=self.additive
+                        )
+        elif self.dataset.type == "Geno":
+            return dict(name=self.name,
+                        dataset=self.dataset.name,
+                        location=self.location_repr
+                        )
+        else:
+            return dict()
                     
 
     def get_name(self):
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 8fc5f120..801266d3 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -4,7 +4,6 @@
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
 {% endblock %}
 {% block content %}
 <!-- Start of body -->
@@ -74,20 +73,26 @@
             <button class="btn" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Remove Record</button>
             <br />
             <br />
+            <form id="export_form" method="POST" action="/export_traits_csv">
+              <input type="hidden" name="database_name" id="database_name" value="None">
+              <input type="hidden" name="export_data" id="export_data" value="">
+              <button class="btn btn-default" id="export_traits">Download CSV</button>
+            </form>
+            <br />
             <div style="background-color: #eeeeee; border: 1px solid black;">
                 <table id="trait_table" class="table table-hover table-striped">
                     <thead>
                         <tr>
                             <th style="background-color: #eeeeee;"></th>
-                            <th style="background-color: #eeeeee;">Index</th>
-                            <th style="background-color: #eeeeee;">Dataset</th>
-                            <th style="background-color: #eeeeee;">Record</th>
-                            <th style="background-color: #eeeeee;">Description</th>
-                            <th style="background-color: #eeeeee;">Location</th>
-                            <th style="background-color: #eeeeee;">Mean</th>
-                            <th style="background-color: #eeeeee;">Max LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00">  ?</sup></a></th>
-                            <th style="background-color: #eeeeee;">Max LRS Location</th>
-                            <th style="background-color: #eeeeee;">Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00">  ?</sup></a></th>
+                            <th data-export="Index" style="background-color: #eeeeee;">Index</th>
+                            <th data-export="Dataset" style="background-color: #eeeeee;">Dataset</th>
+                            <th data-export="Record" style="background-color: #eeeeee;">Record</th>
+                            <th data-export="Description" style="background-color: #eeeeee;">Description</th>
+                            <th data-export="Location" style="background-color: #eeeeee;">Location</th>
+                            <th data-export="Mean" style="background-color: #eeeeee;">Mean</th>
+                            <th data-export="Max LRS" style="background-color: #eeeeee;">Max LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00">  ?</sup></a></th>
+                            <th data-export="Max LRS Location" style="background-color: #eeeeee;">Max LRS Location</th>
+                            <th data-export="Additive Effect" style="background-color: #eeeeee;">Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00">  ?</sup></a></th>
                         </tr>
                     </thead>
 
@@ -98,9 +103,9 @@
                                 <INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox"
                                        VALUE="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}">
                             </TD>
-                            <TD>{{ loop.index }}</TD>
-                            <TD>{{ this_trait.dataset.name }}</TD>
-                            <TD>
+                            <TD data-export="{{ loop.index }}">{{ loop.index }}</TD>
+                            <TD data-export="{{ this_trait.dataset.name }}">{{ this_trait.dataset.name }}</TD>
+                            <TD data-export="{{ this_trait.name }}">
                                 <a href="{{ url_for('show_trait_page',
                                         trait_id = this_trait.name,
                                         dataset = this_trait.dataset.name
@@ -108,12 +113,12 @@
                                     {{ this_trait.name }}
                                 </a>
                             </TD>
-                            <TD>{{ this_trait.description_display }}</TD>
-                            <TD>{{ this_trait.location_repr }}</TD>
-                            <TD>{{ '%0.3f' % this_trait.mean|float }}</TD>
-                            <TD>{{ '%0.3f' % this_trait.LRS_score_repr|float }}</TD>
-                            <TD>{{ this_trait.LRS_location_repr }}</TD>
-                            <TD>{{ '%0.3f' % this_trait.additive|float }}</TD>
+                            <TD data-export="{{ this_trait.description_display }}">{{ this_trait.description_display }}</TD>
+                            <TD data-export="{{ this_trait.location_repr }}">{{ this_trait.location_repr }}</TD>
+                            <TD data-export="{{ this_trait.mean }}">{{ '%0.3f' % this_trait.mean|float }}</TD>
+                            <TD data-export="{{ this_trait.LRS_score_repr }}">{{ '%0.3f' % this_trait.LRS_score_repr|float }}</TD>
+                            <TD data-export="{{ this_trait.LRS_location_repr }}">{{ this_trait.LRS_location_repr }}</TD>
+                            <TD data-export="{{ this_trait.additive }}">{{ '%0.3f' % this_trait.additive|float }}</TD>
 
                         </TR>
                     {% endfor %}
@@ -132,9 +137,6 @@
 {% block js %}
     <script type="text/javascript" src="/static/new/javascript/search_results.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="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/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>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
@@ -170,18 +172,7 @@
                       "width": "15%"  },
                     { "type": "natural" }
                 ],
-                "buttons": [
-                    {
-                       extend: 'csvHtml5',
-                       text: 'Download CSV',
-                       title: 'collection',
-                       fieldBoundary: '"',
-                       exportOptions: {
-                           columns: [1, 2, 3, 4, 5, 6, 7, 8, 9]
-                       }
-                    }
-                ],
-                "sDom": "ZRBtir",
+                "sDom": "ZRtir",
                 "iDisplayLength": -1,
                 "autoWidth": true,
                 "bDeferRender": true,
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 776b8d07..8b8a9057 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -2,7 +2,6 @@
 {% 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="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
 {% endblock %}
 {% block content %}
 <!-- Start of body -->
@@ -99,9 +98,6 @@
     <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     
     <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.12/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/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>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index 9aad7568..2f7dcaf6 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -4,7 +4,6 @@
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.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">
 {% endblock %}
@@ -93,9 +92,6 @@
     <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     
     <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.12/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/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>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index b6aab101..0f5e68d7 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -5,7 +5,6 @@
     <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" />
 {% endblock %}
 {% block content %}
 <!-- Start of body -->
@@ -166,9 +165,6 @@
     <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     
     <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.12/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/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>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
-- 
cgit v1.2.3


From 684f461b815e3920419874fccb036c359cae35d8 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 25 Oct 2016 16:48:54 +0000
Subject: Just removed some extraneous spaces in trait.py

---
 wqflask/base/trait.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 358138f5..276c624a 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -78,7 +78,7 @@ class GeneralTrait(object):
         """Return a dict suitable for using as json
 
         Actual turning into json doesn't happen here though"""
-        
+
         if self.dataset.type == "ProbeSet":
             return dict(name=self.name,
                         symbol=self.symbol,
@@ -108,7 +108,7 @@ class GeneralTrait(object):
                         )
         else:
             return dict()
-                    
+
 
     def get_name(self):
         stringy = ""
-- 
cgit v1.2.3