Added back in some of the options on the trait page; Add, Find, and Verify now work. I'll get the other 4 working next.

6 files changed, 123 insertions, 102 deletions

diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 7ad824fa..adb12b7b 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -362,34 +362,35 @@ class ShowTrait(object):
                 #--------Hongqiang add this part in order to not only blat ProbeSet, but also blat Probe
                 blatsequence = '%3E'+this_trait.name+'%0A'+blatsequence+'%0A'
                 #XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead.
-                self.cursor.execute("""SELECT Probe.Sequence, Probe.Name
+                query = """SELECT Probe.Sequence, Probe.Name
                                        FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef
                                        WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
                                              ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-                                             ProbeSetFreeze.Name = '%s' AND
-                                             ProbeSet.Name = '%s' AND
-                                             Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (this_trait.dataset.name, this_trait.name) )
+                                             ProbeSetFreeze.Name = '{}' AND
+                                             ProbeSet.Name = '{}' AND
+                                             Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""".format(this_trait.dataset.name, this_trait.name)
+
+                seqs = g.db.execute(query).fetchall()
 
-                seqs = self.cursor.fetchall()
                 for seqt in seqs:
                     if int(seqt[1][-1]) %2 == 1:
                         blatsequence += '%3EProbe_'+string.strip(seqt[1])+'%0A'+string.strip(seqt[0])+'%0A'
 
                 #XZ: Pay attention to the parameter of version (rn, mm, hg). They need to be changed if necessary.
                 if _Species == "rat":
-                    UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', blatsequence)
+                    self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', blatsequence)
                     UTHSC_BLAT_URL = ""
                 elif _Species == "mouse":
-                    UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', blatsequence)
+                    self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', blatsequence)
                     UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', blatsequence)
                 elif _Species == "human":
-                    UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence)
+                    self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence)
                     UTHSC_BLAT_URL = ""
                 else:
-                    UCSC_BLAT_URL = ""
+                    self.UCSC_BLAT_URL = ""
                     UTHSC_BLAT_URL = ""
 
-                if UCSC_BLAT_URL:
+                if self.UCSC_BLAT_URL != "":
                     verifyButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UCSC_BLAT_URL)
                     verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ",
                             title=" Check probe locations at UCSC ", style="border:none;")
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index 3dedd7d5..91aa15ba 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -61,6 +61,14 @@ Stat_Table_Rows = [
         ]
 
 $ ->
+
+    add = ->
+        trait = $("input[name=trait_hmac]").val()
+        console.log("trait is:", trait)
+        $.colorbox({href:"/collections/add?traits=#{trait}"})
+
+    $('#add_to_collection').click(add)
+
     sample_lists = js_data.sample_lists
     sample_group_types = js_data.sample_group_types
 
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 7311d0a8..302d5ec4 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -1,8 +1,8 @@
-// Generated by CoffeeScript 1.9.2
+// Generated by CoffeeScript 1.8.0
 (function() {
   var Stat_Table_Rows, is_number,
-    hasProp = {}.hasOwnProperty,
-    slice = [].slice;
+    __hasProp = {}.hasOwnProperty,
+    __slice = [].slice;
 
   console.log("start_b");
 
@@ -56,7 +56,16 @@
   ];
 
   $(function() {
-    var block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, export_sample_table_data, get_sample_table_data, hide_no_value, hide_tabs, make_table, on_corr_method_change, open_trait_selection, populate_sample_attributes_values_dropdown, process_id, redraw_bar_chart, redraw_histogram, redraw_prob_plot, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values;
+    var add, block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, export_sample_table_data, get_sample_table_data, hide_no_value, hide_tabs, make_table, on_corr_method_change, open_trait_selection, populate_sample_attributes_values_dropdown, process_id, redraw_bar_chart, redraw_histogram, redraw_prob_plot, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values;
+    add = function() {
+      var trait;
+      trait = $("input[name=trait_hmac]").val();
+      console.log("trait is:", trait);
+      return $.colorbox({
+        href: "/collections/add?traits=" + trait
+      });
+    };
+    $('#add_to_collection').click(add);
     sample_lists = js_data.sample_lists;
     sample_group_types = js_data.sample_group_types;
     d3.select("#select_compare_trait").on("click", (function(_this) {
@@ -82,12 +91,12 @@
       })(this));
     };
     hide_tabs = function(start) {
-      var i, ref, results, x;
-      results = [];
-      for (x = i = ref = start; ref <= 10 ? i <= 10 : i >= 10; x = ref <= 10 ? ++i : --i) {
-        results.push($("#stats_tabs" + x).hide());
+      var x, _i, _results;
+      _results = [];
+      for (x = _i = start; start <= 10 ? _i <= 10 : _i >= 10; x = start <= 10 ? ++_i : --_i) {
+        _results.push($("#stats_tabs" + x).hide());
       }
-      return results;
+      return _results;
     };
     stats_mdp_change = function() {
       var selected;
@@ -124,36 +133,36 @@
       }
     };
     update_stat_values = function(sample_sets) {
-      var category, i, len, ref, results, row, show_effects;
+      var category, row, show_effects, _i, _len, _ref, _results;
       show_effects = $(".tab-pane.active").attr("id") === "stats_tab";
-      ref = ['samples_primary', 'samples_other', 'samples_all'];
-      results = [];
-      for (i = 0, len = ref.length; i < len; i++) {
-        category = ref[i];
-        results.push((function() {
-          var j, len1, results1;
-          results1 = [];
-          for (j = 0, len1 = Stat_Table_Rows.length; j < len1; j++) {
-            row = Stat_Table_Rows[j];
+      _ref = ['samples_primary', 'samples_other', 'samples_all'];
+      _results = [];
+      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+        category = _ref[_i];
+        _results.push((function() {
+          var _j, _len1, _results1;
+          _results1 = [];
+          for (_j = 0, _len1 = Stat_Table_Rows.length; _j < _len1; _j++) {
+            row = Stat_Table_Rows[_j];
             console.log("Calling change_stats_value");
-            results1.push(change_stats_value(sample_sets, category, row.vn, row.digits, show_effects));
+            _results1.push(change_stats_value(sample_sets, category, row.vn, row.digits, show_effects));
           }
-          return results1;
+          return _results1;
         })());
       }
-      return results;
+      return _results;
     };
     redraw_histogram = function() {
       var x;
       return root.histogram.redraw((function() {
-        var i, len, ref, results;
-        ref = _.values(root.selected_samples[root.histogram_group]);
-        results = [];
-        for (i = 0, len = ref.length; i < len; i++) {
-          x = ref[i];
-          results.push(x.value);
+        var _i, _len, _ref, _results;
+        _ref = _.values(root.selected_samples[root.histogram_group]);
+        _results = [];
+        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+          x = _ref[_i];
+          _results.push(x.value);
         }
-        return results;
+        return _results;
       })());
     };
     redraw_bar_chart = function() {
@@ -163,13 +172,13 @@
       return root.redraw_prob_plot_impl(root.selected_samples, root.prob_plot_group);
     };
     make_table = function() {
-      var header, i, key, len, ref, ref1, row, row_line, table, the_id, the_rows, value;
+      var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1;
       header = "<thead><tr><th>&nbsp;</th>";
       console.log("js_data.sample_group_types:", js_data.sample_group_types);
-      ref = js_data.sample_group_types;
-      for (key in ref) {
-        if (!hasProp.call(ref, key)) continue;
-        value = ref[key];
+      _ref = js_data.sample_group_types;
+      for (key in _ref) {
+        if (!__hasProp.call(_ref, key)) continue;
+        value = _ref[key];
         console.log("aa key:", key);
         console.log("aa value:", value);
         the_id = process_id("column", key);
@@ -178,8 +187,8 @@
       header += "</thead>";
       console.log("windex header is:", header);
       the_rows = "<tbody>";
-      for (i = 0, len = Stat_Table_Rows.length; i < len; i++) {
-        row = Stat_Table_Rows[i];
+      for (_i = 0, _len = Stat_Table_Rows.length; _i < _len; _i++) {
+        row = Stat_Table_Rows[_i];
         console.log("rowing");
         row_line = "<tr>";
         if (row.url != null) {
@@ -188,10 +197,10 @@
           row_line += "<td id=\"" + row.vn + "\">" + row.pretty + "</td>";
         }
         console.log("box - js_data.sample_group_types:", js_data.sample_group_types);
-        ref1 = js_data.sample_group_types;
-        for (key in ref1) {
-          if (!hasProp.call(ref1, key)) continue;
-          value = ref1[key];
+        _ref1 = js_data.sample_group_types;
+        for (key in _ref1) {
+          if (!__hasProp.call(_ref1, key)) continue;
+          value = _ref1[key];
           console.log("apple key:", key);
           the_id = process_id(key, row.vn);
           console.log("the_id:", the_id);
@@ -207,13 +216,13 @@
       return $("#stats_table").append(table);
     };
     process_id = function() {
-      var i, len, processed, value, values;
-      values = 1 <= arguments.length ? slice.call(arguments, 0) : [];
+      var processed, value, values, _i, _len;
+      values = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
 
       /* Make an id or a class valid javascript by, for example, eliminating spaces */
       processed = "";
-      for (i = 0, len = values.length; i < len; i++) {
-        value = values[i];
+      for (_i = 0, _len = values.length; _i < _len; _i++) {
+        value = values[_i];
         console.log("value:", value);
         value = value.replace(" ", "_");
         if (processed.length) {
@@ -224,7 +233,7 @@
       return processed;
     };
     edit_data_change = function() {
-      var already_seen, checkbox, checked, i, j, len, len1, name, real_dict, real_value, real_variance, row, rows, sample_sets, table, tables;
+      var already_seen, checkbox, checked, name, real_dict, real_value, real_variance, row, rows, sample_sets, table, tables, _i, _j, _len, _len1;
       already_seen = {};
       sample_sets = {
         samples_primary: new Stats([]),
@@ -238,11 +247,11 @@
       };
       console.log("at beginning:", sample_sets);
       tables = ['samples_primary', 'samples_other'];
-      for (i = 0, len = tables.length; i < len; i++) {
-        table = tables[i];
+      for (_i = 0, _len = tables.length; _i < _len; _i++) {
+        table = tables[_i];
         rows = $("#" + table).find('tr');
-        for (j = 0, len1 = rows.length; j < len1; j++) {
-          row = rows[j];
+        for (_j = 0, _len1 = rows.length; _j < _len1; _j++) {
+          row = rows[_j];
           name = $(row).find('.edit_sample_sample_name').html();
           name = $.trim(name);
           real_value = $(row).find('.edit_sample_value').val();
@@ -310,26 +319,26 @@
       return "<option val=" + value + ">" + value + "</option>";
     };
     populate_sample_attributes_values_dropdown = function() {
-      var attribute_info, i, key, len, ref, ref1, results, sample_attributes, selected_attribute, value;
+      var attribute_info, key, sample_attributes, selected_attribute, value, _i, _len, _ref, _ref1, _results;
       console.log("in beginning of psavd");
       $('#attribute_values').empty();
       sample_attributes = {};
-      ref = js_data.attribute_names;
-      for (key in ref) {
-        if (!hasProp.call(ref, key)) continue;
-        attribute_info = ref[key];
+      _ref = js_data.attribute_names;
+      for (key in _ref) {
+        if (!__hasProp.call(_ref, key)) continue;
+        attribute_info = _ref[key];
         sample_attributes[attribute_info.name] = attribute_info.distinct_values;
       }
       console.log("[visa] attributes is:", sample_attributes);
       selected_attribute = $('#exclude_menu').val().replace("_", " ");
       console.log("selected_attribute is:", selected_attribute);
-      ref1 = sample_attributes[selected_attribute];
-      results = [];
-      for (i = 0, len = ref1.length; i < len; i++) {
-        value = ref1[i];
-        results.push($(create_value_dropdown(value)).appendTo($('#attribute_values')));
+      _ref1 = sample_attributes[selected_attribute];
+      _results = [];
+      for (_i = 0, _len = _ref1.length; _i < _len; _i++) {
+        value = _ref1[_i];
+        _results.push($(create_value_dropdown(value)).appendTo($('#attribute_values')));
       }
-      return results;
+      return _results;
     };
     if (js_data.attribute_names.length > 0) {
       populate_sample_attributes_values_dropdown();
@@ -352,17 +361,17 @@
     };
     $('#exclude_group').click(block_by_attribute_value);
     block_by_index = function() {
-      var end_index, error, i, index, index_list, index_set, index_string, j, k, len, len1, ref, ref1, ref2, results, start_index;
+      var end_index, error, index, index_list, index_set, index_string, start_index, _i, _j, _k, _len, _len1, _ref, _results;
       index_string = $('#remove_samples_field').val();
       index_list = [];
-      ref = index_string.split(",");
-      for (i = 0, len = ref.length; i < len; i++) {
-        index_set = ref[i];
+      _ref = index_string.split(",");
+      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+        index_set = _ref[_i];
         if (index_set.indexOf('-') !== -1) {
           try {
             start_index = parseInt(index_set.split("-")[0]);
             end_index = parseInt(index_set.split("-")[1]);
-            for (index = j = ref1 = start_index, ref2 = end_index; ref1 <= ref2 ? j <= ref2 : j >= ref2; index = ref1 <= ref2 ? ++j : --j) {
+            for (index = _j = start_index; start_index <= end_index ? _j <= end_index : _j >= end_index; index = start_index <= end_index ? ++_j : --_j) {
               index_list.push(index);
             }
           } catch (_error) {
@@ -376,22 +385,22 @@
         }
       }
       console.log("index_list:", index_list);
-      results = [];
-      for (k = 0, len1 = index_list.length; k < len1; k++) {
-        index = index_list[k];
+      _results = [];
+      for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) {
+        index = index_list[_k];
         if ($('#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"));
+          _results.push($('#Primary_' + index.toString()).find('.trait_value_input').val("x"));
         } else if ($('#block_group').val() === "other") {
           console.log("block_group:", $('#block_group').val());
           console.log("row:", $('#Other_' + index.toString()));
-          results.push($('#Other_' + index.toString()).find('.trait_value_input').val("x"));
+          _results.push($('#Other_' + index.toString()).find('.trait_value_input').val("x"));
         } else {
-          results.push(void 0);
+          _results.push(void 0);
         }
       }
-      return results;
+      return _results;
     };
     $('#block_by_index').click(block_by_index);
     hide_no_value = function() {
@@ -428,17 +437,17 @@
       samples = [];
       $('#' + table_name).find('.value_se').each((function(_this) {
         return function(_index, element) {
-          var attribute_info, key, ref, row_data;
+          var attribute_info, key, row_data, _ref;
           row_data = {};
           row_data.name = $.trim($(element).find('.column_name-Sample').text());
           row_data.value = $(element).find('.edit_sample_value').val();
           if ($(element).find('.edit_sample_se').length !== -1) {
             row_data.se = $(element).find('.edit_sample_se').val();
           }
-          ref = js_data.attribute_names;
-          for (key in ref) {
-            if (!hasProp.call(ref, key)) continue;
-            attribute_info = ref[key];
+          _ref = js_data.attribute_names;
+          for (key in _ref) {
+            if (!__hasProp.call(_ref, key)) continue;
+            attribute_info = _ref[key];
             row_data[attribute_info.name] = $.trim($(element).find('.column_name-' + attribute_info.name.replace(" ", "_")).text());
           }
           console.log("row_data is:", row_data);
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 559650f3..c0a404d9 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -26,6 +26,7 @@
     <form method="post" action="/corr_compute" name="trait_page" id="trait_data_form"
     class="form-horizontal">
         <div id="hidden_inputs">
+        <input type="hidden" name="trait_hmac" value="{{ data_hmac('{}:{}'.format(this_trait.name, dataset.name)) }}">
         {% for key in hddn %}
             <input type="hidden" name="{{ key }}" value="{{ hddn[key] }}">
         {% endfor %}
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index ffedbd5f..c938c683 100755
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -60,38 +60,40 @@
 
 
 
-<!--<div class="btn-toolbar">
+<div style="margin-bottom:15px;" class="btn-toolbar">
     <div class="btn-group">
-        <button class="btn btn-primary" title="Add to collection">
+        <button type="button" id="add_to_collection" class="btn btn-primary" title="Add to collection">
             <i class="icon-plus-sign icon-white"></i> Add
         </button>
-
-        <button class="btn" title="Find similar expression data">
+        <a href="#redirect" onclick="window.open('http://www.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene=Shh&amp;alias=1&amp;species=mouse')">
+        <button type="button" class="btn btn-default" title="Find similar expression data">
             <i class="icon-search"></i> Find
         </button>
-
-        <button class="btn" title="Check probe locations at UCSC">
+        </a>
+        <a href="#redirect" onclick="window.open('{{ UCSC_BLAT_URL }}')">
+        <button type="button" class="btn btn-default" title="Check probe locations at UCSC">
             <i class="icon-ok"></i> Verify
         </button>
+        </a>
     </div>
 
     <div class="btn-group">
 
-        <button class="btn" title="Write or review comments about this gene">
+        <button type="button" class="btn btn-default" title="Write or review comments about this gene">
             <i class="icon-edit"></i> GeneWiki
         </button>
 
-        <button class="btn" title="View SNPs and Indels">
+        <button type="button" class="btn btn-default" title="View SNPs and Indels">
             <i class="icon-road"></i> SNPs
         </button>
 
-        <button class="btn" title="View probes, SNPs, and RNA-seq at UTHSC">
+        <button type="button" class="btn btn-default" title="View probes, SNPs, and RNA-seq at UTHSC">
             <i class="icon-eye-close"></i> RNA-seq
         </button>
 
-        <button class="btn" title="Check sequence of probes">
+        <button type="button" class="btn btn-default" title="Check sequence of probes">
             <i class="icon-list"></i> Probes
         </button>
 
     </div>
-</div>-->
+</div>
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 585165bb..a02dc409 100755
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -44,11 +44,11 @@
             {% endif %}
             <br>
             <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">
+              <input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value">
+              <input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers">
+              <input type="button" id="reset" class="btn btn-primary" value="Reset">
               <span class="input-append">
-                <input type="button" id="export" class="btn" value="Export">
+                <input type="button" id="export" class="btn btn-default" value="Export">
                 <select id="export_format" class="select optional span2">
                   <option value="excel">Excel</option>
                   <option value="csv">CSV</option>