Fixed bug in an SQL query, changed search field id from "ORkeyword" to "search_terms"

9 files changed, 87 insertions, 66 deletions

diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py
index 67325b56..e34992a0 100644
--- a/wqflask/wqflask/parser.py
+++ b/wqflask/wqflask/parser.py
@@ -36,10 +36,11 @@ def parse(pstring):
     print(pf(items))
     return(items)
     
-parse("foo=(3 2 1)")
-parse("shh")
-parse("shh grep")
-parse("LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)")
-parse("sal1 LRS=(9 99 Chr4 122 155) sal2 cisLRS=(9 999 10)")
-parse("sal1 sal3 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9 999 10)")
-parse("sal1 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9, 999, 10)")
\ No newline at end of file
+if __name__ == '__main__':
+    parse("foo=(3 2 1)")
+    parse("shh")
+    parse("shh grep")
+    parse("LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)")
+    parse("sal1 LRS=(9 99 Chr4 122 155) sal2 cisLRS=(9 999 10)")
+    parse("sal1 sal3 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9 999 10)")
+    parse("sal1 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9, 999, 10)")
\ No newline at end of file
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 4cca6492..585deb8f 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -60,6 +60,7 @@ class SearchResultPage(templatePage):
     nkeywords = 0
 
     def __init__(self, fd):
+        self.fd = fd
         if not self.openMysql():
             return
 
@@ -98,9 +99,15 @@ class SearchResultPage(templatePage):
                 #userExist = None
 
                 for individualDB in self.database:
-                    self.cursor.execute('''SELECT Id, Name, FullName, confidentiality,
-                                        AuthorisedUsers FROM %sFreeze WHERE Name = %s''', (
-                                        self.database[0].type, individualDB))
+                    # Can't use paramater substitution for table names apparently
+                    db_type = self.database[0].type + "Freeze"
+                    print("db_type [%s]: %s" % (type(db_type), db_type))
+                    
+                    query = '''SELECT Id, Name, FullName, confidentiality,
+                                        AuthorisedUsers FROM %s WHERE Name = %%s''' % (db_type)
+                    
+                    self.cursor.execute(query, (individualDB,))
+                    
                     (indId,
                      indName,
                      indFullName,
@@ -175,6 +182,8 @@ class SearchResultPage(templatePage):
                                 'RefSeq_TranscriptId']
         elif self.dbType == "Geno":
             self.searchField = ['Name','Chr']
+            
+        self.do_search()
 
         ###########################################
         #       Search Options
@@ -545,7 +554,6 @@ class SearchResultPage(templatePage):
 
         _log.info("Done executing queries")
 
-
         #searchCountQuery retrieve all the results, for counting use only
         if searchCountQuery != searchQuery:
             for item in searchQuery:
@@ -558,7 +566,6 @@ class SearchResultPage(templatePage):
         return nresults
 
 
-
     def assembleQuery(self):
         self.query = []
         if self.ANDQuery or self.ORQuery:
@@ -635,13 +642,15 @@ class SearchResultPage(templatePage):
             return 0
 
 
+    def do_search(self):
+        print("fd.search_terms:", self.fd['search_terms'])
+        self.search_terms = parser.parse(self.fd['search_terms'])
+        print("After parsing:", self.search_terms)
+        #print("ORkeyword is:", pf(self.ORkeyword))
+        #self.ANDkeyword2 = parser.parse(self.ANDkeyword)
+        #self.ORkeyword2 = parser.parse(self.ORkeyword)
+        #print("ORkeyword2 is:", pf(parser.parse(self.ORkeyword)))
 
-    def normalSearch(self):
-        print("ORkeyword is:", pf(self.ORkeyword))
-        self.ANDkeyword2 = parser.parse(self.ANDkeyword)
-        self.ORkeyword2 = parser.parse(self.ORkeyword)
-        print("ORkeyword2 is:", pf(parser.parse(self.ORkeyword)))
-        
         #self.ANDkeyword2 = re.sub(self._1mPattern, '', self.ANDkeyword)
         #self.ANDkeyword2 = re.sub(self._2mPattern, '', self.ANDkeyword2)
         #self.ANDkeyword2 = re.sub(self._3mPattern, '', self.ANDkeyword2)
@@ -649,7 +658,7 @@ class SearchResultPage(templatePage):
         ###remove remain parethesis, could be input with  syntax error
         #self.ANDkeyword2 = re.sub(re.compile('\s*\([\s\S]*\)'), '', self.ANDkeyword2)
         #self.ANDkeyword2 = self.encregexp(self.ANDkeyword2)
-        #
+
         #self.ORkeyword2 = re.sub(self._1mPattern, '', self.ORkeyword)
         #self.ORkeyword2 = re.sub(self._2mPattern, '', self.ORkeyword2)
         #self.ORkeyword2 = re.sub(self._3mPattern, '', self.ORkeyword2)
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py
index e5f2035d..f7f2d6d4 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/wqflask/wqflask/show_trait/export_trait_data.py
@@ -4,21 +4,13 @@ import operator
 
 import simplejson as json
 
-#import xlwt
 from pprint import pformat as pf
 
 def export_sample_table(targs):
-    #print("* keys0 args is:", targs[0].keys())
-    
-    
-    #test_export_file = open("/home/zas1024/gene/wqflask/wqflask/show_trait/export_test.txt", "w")
-    #
-    #for key, item in targs.iteritems():
-    #    print("[arrow] key is:", key)
-    
+
     sample_data = json.loads(targs['export_data'])
     final_sample_data = []
-    
+
     for sample_group in ['primary_samples', 'other_samples']:
         for row in sample_data[sample_group]:
             sorted_row = dict_to_sorted_list(row)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index c7dc7c88..b1cca461 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -295,6 +295,10 @@ $ ->
         samples.other_samples = other_samples
         return samples
 
+    ##End Get Sample Data from Table Code
+
+    ##Export Sample Table Data Code
+    
     export_sample_table_data = ->
         sample_data = get_sample_table_data()
         console.log("sample_data is:", sample_data)
@@ -302,27 +306,19 @@ $ ->
         console.log("json_sample_data is:", json_sample_data)
         
         $('input[name=export_data]').val(json_sample_data)
-        
         console.log("export_data is", $('input[name=export_data]').val())
         
-        $('#trait_data_form').attr('action', '/export_trait_csv')
+        format = $('#export_format').val()
+        if format == "excel"
+            $('#trait_data_form').attr('action', '/export_trait_excel')
+        else
+            $('#trait_data_form').attr('action', '/export_trait_csv')
         console.log("action is:", $('#trait_data_form').attr('action'))
+        
         $('#trait_data_form').submit()
-         
-        #$.ajax(
-        #    url: '/export_trait_csv'
-        #    type: 'POST'
-        #    data: "json_data=" + json_sample_data
-        #)
 
     $('#export').click(export_sample_table_data)
     
-    
-
-    ##End Get Sample Data from Table Code
-
-    ##Export Sample Table Data Code
-    
     ##End Export Sample Table Data Code
 
 
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 5729eb22..5aadedef 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -334,14 +334,19 @@
       return samples;
     };
     export_sample_table_data = function() {
-      var json_sample_data, sample_data;
+      var format, json_sample_data, sample_data;
       sample_data = get_sample_table_data();
       console.log("sample_data is:", sample_data);
       json_sample_data = JSON.stringify(sample_data);
       console.log("json_sample_data is:", json_sample_data);
       $('input[name=export_data]').val(json_sample_data);
       console.log("export_data is", $('input[name=export_data]').val());
-      $('#trait_data_form').attr('action', '/export_trait_csv');
+      format = $('#export_format').val();
+      if (format === "excel") {
+        $('#trait_data_form').attr('action', '/export_trait_excel');
+      } else {
+        $('#trait_data_form').attr('action', '/export_trait_csv');
+      }
       console.log("action is:", $('#trait_data_form').attr('action'));
       return $('#trait_data_form').submit();
     };
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index a209f302..db0b2d9e 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -96,7 +96,7 @@
                     <td width="3%"></td>
 
                     <td nowrap width="85%" align="left"><input class="input-medium search-query"
-                    id="tfor" name="ORkeyword" style=
+                    id="tfor" name="search_terms" style=
                     "width:420px; background-color:white; font-family:verdana; font-size:14px"
                     type="text" maxlength="500"></td>
                   </tr><!--  GET ANY HELP   -->
diff --git a/wqflask/wqflask/templates/new_index_page.html b/wqflask/wqflask/templates/new_index_page.html
index 3d6d3f3f..f2178f3c 100644
--- a/wqflask/wqflask/templates/new_index_page.html
+++ b/wqflask/wqflask/templates/new_index_page.html
@@ -125,7 +125,7 @@
                             <label for="tfor">Search:</label>
 
                             <input class="search-query"
-                                id="tfor" name="ORkeyword"
+                                id="tfor" name="search_terms"
                                 type="text" maxlength="500">
 
                             <!--  GET ANY HELP   -->
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 1e1d8b8f..d48f9487 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -1253,10 +1253,18 @@
                             </div>
                             {% endif %}
                             <br>
-                            <input type="button" id="hide_no_value" class="btn" value="Hide No Value">
-                            <input type="button" id="block_outliers" class="btn" value="Block Outliers">
-                            <input type="button" id="reset" class="btn btn-inverse" value="Reset">
-                            <input type="button" id="export" class="btn" value="Export">
+                            <div>
+                              <input type="button" id="hide_no_value" class="btn" value="Hide No Value">
+                              <input type="button" id="block_outliers" class="btn" value="Block Outliers">
+                              <input type="button" id="reset" class="btn btn-inverse" value="Reset">
+                              <span class="input-append">
+                                <input type="button" id="export" class="btn" value="Export">
+                                <select id="export_format" class="select optional span2">
+                                  <option value="excel">Excel</option>
+                                  <option value="csv">CSV</option>
+                                </select>                                                      
+                              </span>             
+                            </div>                   
                         </fieldset>
                         <br>
                         <div>
@@ -1272,17 +1280,16 @@
                         </div>
                         </div>
                         <br>
-                        
-                  
-                        
-                        
+
+
+
                         <div style="width:80%;margin:0;padding:0;border:none;">
                         {% for sample_type in sample_groups %}
                         <div style="float:left;width:50%;">
                         <h2>{{ sample_type.header }}</h2>
                             
                         <div id="{{ sample_type.sample_group_type }}">  
-                          <table class="not_tablesorter"  {# Todo: Turn tablesorter back on #}
+                          <table class="table table-hover not_tablesorter"  {# Todo: Turn tablesorter back on #}
                                  id="{{ 'sortable%i' % (loop.index) }}"
                                  cellpadding="0" cellspacing="0">
                             <tr>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 693b863a..2933b428 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -90,6 +90,25 @@ def show_trait_page():
     print("show_trait template_vars:", pf(template_vars.__dict__))
     return render_template("show_trait.html", **template_vars.__dict__)
 
+@app.route('/export_trait_csv', methods=('POST',))
+def export_trait_excel():
+    """Excel file consisting of the sample data from the trait data and analysis page"""
+    print("In export_trait_excel")
+    print("request.form:", request.form)
+    sample_data = export_trait_data.export_sample_table(request.form)
+
+    print("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data)))
+
+    buff = StringIO.StringIO()
+    writer = csv.writer(buff)
+    for row in sample_data:
+        writer.writerow(row)
+    csv_data = buff.getvalue()
+    buff.close()
+
+    return Response(csv_data,
+                    mimetype='text/csv',
+                    headers={"Content-Disposition":"attachment;filename=test.csv"})
 
 @app.route('/export_trait_csv', methods=('POST',))
 def export_trait_csv():
@@ -97,7 +116,7 @@ def export_trait_csv():
     print("In export_trait_csv")
     print("request.form:", request.form)
     sample_data = export_trait_data.export_sample_table(request.form)
-    
+
     print("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data)))
 
     buff = StringIO.StringIO()
@@ -106,20 +125,12 @@ def export_trait_csv():
         writer.writerow(row)
     csv_data = buff.getvalue()
     buff.close()
-                    
+
     return Response(csv_data,
                     mimetype='text/csv',
                     headers={"Content-Disposition":"attachment;filename=test.csv"})
 
 
-#@app.route("/export_trait_data", methods=('POST',))
-#def export_sample_table():
-#    """CSV file consisting of the sample data from the trait data and analysis page"""
-#    print("In export_sample_table")
-#    print("request.form:", request.form)
-#    template_vars = export_trait_data.export_sample_table(request.form)
-
-
 @app.route("/corr_compute", methods=('POST',))
 def corr_compute_page():
     #print("In corr_compute, request.args is:", pf(request.form))