Began changes to search result page python code

4 files changed, 149 insertions, 56 deletions

diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index d393d0c1..a9972349 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -771,37 +771,40 @@ class SearchResultPage(templatePage):
                         DescriptionText = self.ORDescriptionText
 
                     itemCmd = item[0]
-                    lowerLimit = float(item[1])
-                    upperLimit = float(item[2])
+                    lower_limit = float(item[1])
+                    upper_limit = float(item[2])
 
                     if itemCmd.upper() in ("TRANSLRS", "CISLRS"):
                         if item[3]:
                             mthresh = float(item[3])
                             clauseItem = " %sXRef.LRS > %2.7f and %sXRef.LRS < %2.7f " % \
-                                (self.dbType, min(lowerLimit, upperLimit), self.dbType, max(lowerLimit, upperLimit))
+                                (self.dbType, min(lower_limit, upper_limit), self.dbType, max(lower_limit, upper_limit))
                             if itemCmd.upper() == "CISLRS":
                                 clauseItem += """ and  %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and %s.Chr = Geno.Chr and ABS(%s.Mb-Geno.Mb) < %2.7f """ % (self.dbType, self.speciesId, self.dbType, self.dbType, mthresh)
-                                DescriptionText.append(HT.Span(' with a ', HT.U('cis-QTL'), ' having an LRS between %g and %g using a %g Mb exclusion buffer'  % (min(lowerLimit, upperLimit), max(lowerLimit, upperLimit),  mthresh)))
+                                DescriptionText.append(HT.Span(' with a ', HT.U('cis-QTL'), ' having an LRS between %g and %g using a %g Mb exclusion buffer'  % (min(lower_limit, upper_limit), max(lower_limit, upper_limit),  mthresh)))
                             else:
                                 clauseItem += """ and  %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and (%s.Chr != Geno.Chr or (%s.Chr != Geno.Chr and ABS(%s.Mb-Geno.Mb) > %2.7f)) """ % (self.dbType, self.speciesId, self.dbType, self.dbType, self.dbType, mthresh)
-                                DescriptionText.append(HT.Span(' with a ', HT.U('trans-QTL'), ' having an LRS between %g and %g using a %g Mb exclusion buffer'  % (min(lowerLimit, upperLimit), max(lowerLimit, upperLimit),  mthresh)))
+                                DescriptionText.append(HT.Span(' with a ', HT.U('trans-QTL'), ' having an LRS between %g and %g using a %g Mb exclusion buffer'  % (min(lower_limit, upper_limit), max(lower_limit, upper_limit),  mthresh)))
                             query.append(" (%s) " % clauseItem)
                             self.orderByDefalut = "LRS"
                         else:
                             pass
                     elif itemCmd.upper() in ("RANGE"):
                         #XZ, 03/05/2009: Xiaodong changed Data to ProbeSetData
-                        clauseItem = " (select Pow(2, max(value) -min(value)) from ProbeSetData where Id = ProbeSetXRef.dataId) > %2.7f and (select Pow(2, max(value) -min(value)) from ProbeSetData where Id = ProbeSetXRef.dataId) < %2.7f " % (min(lowerLimit, upperLimit), max(lowerLimit, upperLimit))
+                        clauseItem = " (select Pow(2, max(value) -min(value)) from ProbeSetData where Id = ProbeSetXRef.dataId) > %2.7f and (select Pow(2, max(value) -min(value)) from ProbeSetData where Id = ProbeSetXRef.dataId) < %2.7f " % (min(lower_limit, upper_limit), max(lower_limit, upper_limit))
                         query.append(" (%s) " % clauseItem)
-                        DescriptionText.append(HT.Span(' with a range of expression that varied between %g and %g' % (min(lowerLimit, upperLimit),  max(lowerLimit, upperLimit)), "  (fold difference)"))
+                        DescriptionText.append(HT.Span(' with a range of expression that varied between %g and %g' % (min(lower_limit, upper_limit),  max(lower_limit, upper_limit)), "  (fold difference)"))
                     else:
                         clauseItem = " %sXRef.%s > %2.7f and %sXRef.%s < %2.7f " % \
-                            (self.dbType, itemCmd, min(lowerLimit, upperLimit), self.dbType, itemCmd, max(lowerLimit, upperLimit))
+                            (self.dbType, itemCmd, min(lower_limit, upper_limit), self.dbType, itemCmd, max(lower_limit, upper_limit))
                         query.append(" (%s) " % clauseItem)
                         self.orderByDefalut = itemCmd
-                        DescriptionText.append(HT.Span(' with ', HT.U(itemCmd), ' between %g and %g' % (min(lowerLimit, upperLimit),  max(lowerLimit, upperLimit))))
+                        DescriptionText.append(HT.Span(' with ', HT.U(itemCmd), ' between %g and %g' % (min(lower_limit, upper_limit),  max(lower_limit, upper_limit))))
 
                 for k, item in enumerate(m3_OR+m3_AND):
+                    print("enumerating m3_OR+m3_AND with k: %s - item %s" % (k, item))
+                    if self.dbType not in ("ProbeSet", "Geno"):
+                        continue
                     if k >=len(m3_OR):
                         query = self.ANDQuery
                         DescriptionText = self.ANDDescriptionText
@@ -809,23 +812,32 @@ class SearchResultPage(templatePage):
                         query = self.ORQuery
                         DescriptionText = self.ORDescriptionText
                     itemCmd = item[0]
-                    chrsch = item[1]
-                    lowerLimit = float(item[2])
-                    upperLimit = float(item[3])
-                    fname = 'target genes'
+                    
+        
+                    chr_number = item[1]     # chromosome number
+                    lower_limit = float(item[2])
+                    upper_limit = float(item[3])
+                    
                     if self.dbType == "ProbeSet":
-                        clauseItem = " %s.Chr = '%s' and %s.Mb > %2.7f and %s.Mb < %2.7f " % \
-                            (self.dbType, chrsch, self.dbType, min(lowerLimit, upperLimit), self.dbType, max(lowerLimit, upperLimit))
+                        fname = 'target genes'
                     elif self.dbType == "Geno":
                         fname = 'loci'
-                        clauseItem = " %s.Chr = '%s' and %s.Mb > %2.7f and %s.Mb < %2.7f " % \
-                            (self.dbType, chrsch, self.dbType, min(lowerLimit, upperLimit), self.dbType, max(lowerLimit, upperLimit))
-                    else:
-                        continue
+                    
+                    if lower_limit > upper_limit:
+                        lower_limit, upper_limit = upper_limit, lower_limit
+                    
+                    
+                    
+                    clauseItem = " %s.Chr = '%s' and %s.Mb > %2.7f and %s.Mb < %2.7f " % (
+                            self.dbType, chr_number, self.dbType, lower_limit, self.dbType, upper_limit)
+                    
+               
                     query.append(" (%s) " % clauseItem)
                     self.orderByDefalut = itemCmd
-                    DescriptionText.append(HT.Span(' with ', HT.U('target genes'), ' on chromosome %s between %g and %g Mb' % \
-                        (chrsch, min(lowerLimit, upperLimit), max(lowerLimit, upperLimit))))
+                    
+                    self.results_desc = dict() 
+                    #DescriptionText.append(HT.Span(' with ', HT.U('target genes'), ' on chromosome %s between %g and %g Mb' % \
+                    #    (chr_number, min(lower_limit, upper_limit), max(lower_limit, upper_limit))))
 
                 for k, item in enumerate(m5_OR+m5_AND):
                     if k >=len(m5_OR):
@@ -835,22 +847,22 @@ class SearchResultPage(templatePage):
                         query = self.ORQuery
                         DescriptionText = self.ORDescriptionText
                     itemCmd = item[0]
-                    lowerLimit = float(item[1])
-                    upperLimit = float(item[2])
-                    chrsch = item[3]
-                    MblowerLimit = float(item[4])
-                    MbupperLimit = float(item[5])
+                    lower_limit = float(item[1])
+                    upper_limit = float(item[2])
+                    chr_number = item[3]
+                    mb_lower_limit = float(item[4])
+                    mb_upper_limit = float(item[5])
                     if self.dbType == "ProbeSet" or self.dbType == "Publish":
                         clauseItem = " %sXRef.LRS > %2.7f and %sXRef.LRS < %2.7f " % \
-                            (self.dbType, min(lowerLimit, upperLimit), self.dbType, max(lowerLimit, upperLimit))
+                            (self.dbType, min(lower_limit, upper_limit), self.dbType, max(lower_limit, upper_limit))
                         clauseItem += " and  %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and Geno.Chr = '%s' and Geno.Mb > %2.7f and Geno.Mb < %2.7f" \
-                            % (self.dbType, self.speciesId, chrsch, min(MblowerLimit, MbupperLimit),  max(MblowerLimit, MbupperLimit))
+                            % (self.dbType, self.speciesId, chr_number, min(mb_lower_limit, mb_upper_limit),  max(mb_lower_limit, mb_upper_limit))
                         query.append(" (%s) " % clauseItem)
                         self.orderByDefalut = "MB"
                         DescriptionText.append(HT.Span(' with ', HT.U('LRS'), ' between %g and %g' % \
-                            (min(lowerLimit, upperLimit),  max(lowerLimit, upperLimit)), \
+                            (min(lower_limit, upper_limit),  max(lower_limit, upper_limit)), \
                             ' on chromosome %s between %g and %g Mb' % \
-                            (chrsch, min(MblowerLimit, MbupperLimit),  max(MblowerLimit, MbupperLimit))))
+                            (chr_number, min(mb_lower_limit, mb_upper_limit),  max(mb_lower_limit, mb_upper_limit))))
             pass
 
         return 1
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index 29489fb9..b89e15ce 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -196,28 +196,56 @@ $ ->
         exclude_by_value = $('#attribute_values').val()
         
         cell_class = ".column_name-#{attribute_name}"
-        $(cell_class).each (index, element)=>
+        $(cell_class).each (index, element) =>
             if $.trim($(element).text()) == exclude_by_value
                 row = $(element).parent('tr')
                 $(row).find(".trait_value_input").val("x")
-        
-        #sample_lists = js_data['sample_lists']
-        #console.log("sample_lists is:", sample_lists)
-        #for sample_list in sample_lists
-        #    for sample in sample_list
-        #        console.log("sample is:", sample)
-        #        if sample.extra_attributes[attribute_name] == exclude_by_value
-        #            console.log("is exclude_by_value")
-        #            console.log("sample.name is:", sample.name)
-        #            attr_cell = $('td:contains('+sample.name+')').parent().find('td.column_name-'+ attribute_name)
-        #            console.log("attr_cell is:", attr_cell)
-        #            value_cell = attr_cell.parent().find('td.column_name-Value')
-        #            value_cell.children('input').val("x")
-
 
     $('#exclude_group').click(block_by_attribute_value)
     
     ##End Block Samples By Attribute Value Code
+    
+    ##Block Samples By Index Code
+    block_by_index = ->
+        index_string = $('#remove_samples_field').val()
+        console.log("index_string is:", index_string)
+        index_list = []
+        for index_set in index_string.split(",")
+            if index_set.indexOf('-') != -1
+                try
+                    start_index = parseInt(index_set.split("-")[0])
+                    console.log("start_index:", start_index)
+                    end_index = parseInt(index_set.split("-")[1])
+                    console.log("end_index:", end_index)
+                    index_list.push(index) for index in [start_index..end_index]
+                catch error
+                    alert("Syntax error")
+            else
+                #try
+                    index = parseInt(index_set)
+                    console.log("index:", index)
+                    index_list.push(index)
+                #catch(erro) 
+                #    alert("Syntax error")
+        console.log("index_list:", index_list)
+        for index in index_list
+            if $('#block_group').val() == "primary"
+                console.log("block_group:", $('#block_group').val())
+                console.log("row:", $('#Primary_'+index.toString()))
+                $('#Primary_'+index.toString()).find('.trait_value_input').val("x")
+            else if $('#block_group').val() == "other"
+                $('#Other_'+index.toString()).find('.trait_value_input').val("x")
+    
+    $('#remove_samples_field').validate(
+        rules: 
+            field: 
+                required: true
+                number: true
+    )
+    
+    $('#block_by_index').click(block_by_index)
+
+    ##End Block Samples By Index Code
 
     console.log("before registering show_hide_outliers")
     $('#show_hide_outliers').click(show_hide_outliers)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index a5582519..6d3dee13 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -11,7 +11,7 @@
   };
 
   $(function() {
-    var block_by_attribute_value, change_stats_value, create_value_dropdown, edit_data_change, hide_tabs, make_table, on_corr_method_change, populate_sample_attributes_values_dropdown, process_id, show_hide_outliers, stats_mdp_change, update_stat_values;
+    var block_by_attribute_value, block_by_index, change_stats_value, create_value_dropdown, edit_data_change, hide_tabs, make_table, on_corr_method_change, populate_sample_attributes_values_dropdown, process_id, show_hide_outliers, stats_mdp_change, update_stat_values;
     hide_tabs = function(start) {
       var x, _i, _results;
       _results = [];
@@ -238,6 +238,57 @@
       });
     };
     $('#exclude_group').click(block_by_attribute_value);
+    block_by_index = function() {
+      var end_index, index, index_list, index_set, index_string, start_index, _i, _j, _k, _len, _len1, _ref, _results;
+      index_string = $('#remove_samples_field').val();
+      console.log("index_string is:", index_string);
+      index_list = [];
+      _ref = index_string.split(",");
+      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+        index_set = _ref[_i];
+        if (index_set.indexOf('-') !== -1) {
+          try {
+            start_index = parseInt(index_set.split("-")[0]);
+            console.log("start_index:", start_index);
+            end_index = parseInt(index_set.split("-")[1]);
+            console.log("end_index:", end_index);
+            for (index = _j = start_index; start_index <= end_index ? _j <= end_index : _j >= end_index; index = start_index <= end_index ? ++_j : --_j) {
+              index_list.push(index);
+            }
+          } catch (error) {
+            alert("Syntax error");
+          }
+        } else {
+          index = parseInt(index_set);
+          console.log("index:", index);
+          index_list.push(index);
+        }
+      }
+      console.log("index_list:", index_list);
+      _results = [];
+      for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) {
+        index = index_list[_k];
+        if ($('#block_group').val() === "primary") {
+          console.log("block_group:", $('#block_group').val());
+          console.log("row:", $('#Primary_' + index.toString()));
+          _results.push($('#Primary_' + index.toString()).find('.trait_value_input').val("x"));
+        } else if ($('#block_group').val() === "other") {
+          _results.push($('#Other_' + index.toString()).find('.trait_value_input').val("x"));
+        } else {
+          _results.push(void 0);
+        }
+      }
+      return _results;
+    };
+    $('#remove_samples_field').validate({
+      rules: {
+        field: {
+          required: true,
+          number: true
+        }
+      }
+    });
+    $('#block_by_index').click(block_by_index);
     console.log("before registering show_hide_outliers");
     $('#show_hide_outliers').click(show_hide_outliers);
     console.log("after registering show_hide_outliers");
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index f85cf98e..5a364f8b 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -1214,18 +1214,19 @@
                         <div style=
                         "border: 3px solid #EEEEEE; -moz-border-radius: 10px; -webkit-border-radius: 10px; width: 625px; padding: 5px 5px 10px 8px; font-size: 12px; background: #DDDDDD;">
                         <span id="showHideOptions" style="line-height:225%;"><strong>&nbsp;&nbsp;Block samples by index:&nbsp;&nbsp;&nbsp;&nbsp;</strong>
-                        <input type="text" name="removeField" style=
-                        "background-color:white;border: 1px solid black;font-size: 14px;">&nbsp;&nbsp;&nbsp;<span id="blockMenuSpan"><select name=
-                        "block_method" size="1">
-                            <option value="1">
-                              BXD Only
+                        <input type="text" id="remove_samples_field" style=
+                        "background-color:white;border: 1px solid black;font-size: 14px;">&nbsp;&nbsp;&nbsp;
+                        <span id="blockMenuSpan">
+                          <select id="block_group" size="1">
+                            <option value="primary">
+                              {{ sample_group_types['primary_only'] }}
                             </option>
-
-                            <option value="0">
-                              Non-BXD Only
+                            <option value="other">
+                              {{ sample_group_types['other_only'] }}
                             </option>
-                          </select></span> &nbsp;&nbsp;&nbsp;
-                          <input type="button" name="blockSamples" class="button" value=" Block ">
+                          </select>
+                        </span> &nbsp;&nbsp;&nbsp;
+                          <input type="button" id="block_by_index" class="button" value=" Block ">
                           <br>
 
                           {% if sample_groups[0].attributes %}
@@ -1362,6 +1363,7 @@
 
     <script type="text/javascript" src="/static/new/js_external/underscore-min.js"></script>-->
     <script type="text/javascript" src="/static/new/js_external/underscore.string.min.js"></script>
+    <script type="text/javascript" src="/static/new/packages/ValidationPlugin/dist/jquery.validate.min.js"></script>
     
     <script type="text/javascript" src="/static/new/javascript/stats.js"></script>
     <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>