From cf4db5545efee6d9052153708fc05ca707ef1716 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 24 Nov 2020 12:51:17 -0600
Subject: Added html/css for new "Filter Samples by Value" feature and changed
 a couple class names to make more sense for being shared between both this
 feature and "Block Samples by Index"

---
 wqflask/wqflask/static/new/css/show_trait.css      |  4 ++--
 .../templates/show_trait_transform_and_filter.html | 23 ++++++++++++++++++++--
 2 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 5e1a279b..39c6ba53 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -145,11 +145,11 @@ input.corr-location {
   display: inline;
 }
 
-div.block-by-index-div {
+div.block-div {
   margin-bottom: 10px;
 }
 
-div.block-by-attribute-div {
+div.block-div-2 {
   margin-top:10px;
   margin-bottom:10px;
 }
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index 0418d972..22c52d8c 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -4,7 +4,7 @@
         <strong>Reset</strong> option as
         needed.
     </p>
-    <div id="blockMenuSpan" class="input-append block-by-index-div">
+    <div id="blockMenuSpan" class="input-append block-div">
         <label for="remove_samples_field">Block samples by index:</label>
         <input type="text" id="remove_samples_field" placeholder="Example: 3, 5-10, 12">
         <select id="block_group" size="1">
@@ -20,8 +20,27 @@
     <div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
           Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
     </div>
+    <div id="filterMenuSpan" class="input-append block-div-2">
+      <label for="filter_samples_field">Filter samples by value </label>
+      <select id="filter_logic" size="1">
+        <option value="greater_than">></option>
+        <option value="less_than"><</option>
+        <option value="greater_or_equal">≥</option>
+        <option value="less_or_equal">≤</option>
+      </select>
+      <input type="text" id="filter_value" placeholder="Example: 3, 10, 15">
+      <select id="filter_group" size="1">
+        <option value="primary">
+          {{ sample_group_types['samples_primary'] }}
+        </option>
+        <option value="other">
+          {{ sample_group_types['samples_other'] }}
+        </option>
+      </select>
+      <input type="button" id="filter_by_value" class="btn btn-danger" value="Filter">
+    </div>
     {% if sample_groups[0].attributes %}
-    <div class="input-append block-by-attribute-div">
+    <div class="input-append block-div-2">
         <label for="exclude_menu">Block samples by group:</label>
         <select id="exclude_menu" size=1>
           {% for attribute in sample_groups[0].attributes %}
-- 
cgit v1.2.3


From be315778db1d34f903312b5ac6bcc80dd848a5be Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 24 Nov 2020 12:52:10 -0600
Subject: Added JS for Filter Samples by Value feature and removed a few unused
 lines

---
 .../wqflask/static/new/javascript/show_trait.js    | 49 +++++++++++++++++++++-
 1 file changed, 47 insertions(+), 2 deletions(-)

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index a34811f8..3df8784e 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -608,7 +608,7 @@ block_by_attribute_value = function() {
 };
 $('#exclude_group').click(block_by_attribute_value);
 block_by_index = function() {
-  var end_index, error, index, index_list, index_set, index_string, start_index, _i, _j, _k, _len, _len1, _ref, _results;
+  var end_index, error, index, index_list, index_set, index_string, start_index, _i, _j, _k, _len, _len1, _ref;
   index_string = $('#remove_samples_field').val();
   index_list = [];
   _ref = index_string.split(",");
@@ -630,7 +630,7 @@ block_by_index = function() {
       index_list.push(index);
     }
   }
-  _results = [];
+
   let block_group = $('#block_group').val();
   if (block_group === "other") {
     table_api = $('#samples_other').DataTable();
@@ -645,6 +645,45 @@ block_by_index = function() {
   }
 };
 
+filter_by_value = function() {
+  let filter_logic = $('#filter_logic').val();
+  let filter_value = $('#filter_value').val();
+
+  block_group = $('#filter_group').val();
+  if (block_group === "other") {
+    table_api = $('#samples_other').DataTable();
+  } else {
+    table_api = $('#samples_primary').DataTable();
+  }
+
+  let val_nodes = table_api.column(3).nodes().to$();
+  for (i = 0; i < val_nodes.length; i++) {
+    let this_node = val_nodes[i].childNodes[0];
+    if(!isNaN(this_node.value) && !isNaN(filter_value)) {
+      if (filter_logic == "greater_than"){
+        if (parseFloat(this_node.value) <= parseFloat(filter_value)){
+          this_node.value = "x";
+        }
+      }
+      else if (filter_logic == "less_than"){
+        if (parseFloat(this_node.value) >= parseFloat(filter_value)){
+          this_node.value = "x";
+        }
+      }
+      else if (filter_logic == "greater_or_equal"){
+        if (parseFloat(this_node.value) < parseFloat(filter_value)){
+          this_node.value = "x";
+        }
+      }
+      else if (filter_logic == "less_or_equal"){
+        if (parseFloat(this_node.value) > parseFloat(filter_value)){
+          this_node.value = "x";
+        }
+      }
+    }
+  }
+};
+
 hide_no_value = function() {
   return $('.value_se').each((function(_this) {
     return function(_index, element) {
@@ -1528,6 +1567,12 @@ $('#block_by_index').click(function(){
   block_by_index();
   edit_data_change();
 });
+
+$('#filter_by_value').click(function(){
+  filter_by_value();
+  edit_data_change();
+})
+
 $('#exclude_group').click(edit_data_change);
 $('#block_outliers').click(edit_data_change);
 $('#reset').click(edit_data_change);
-- 
cgit v1.2.3


From 77dc4a4e7c68a10f9b7d743e02a0738cab870c68 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 24 Nov 2020 16:14:20 -0600
Subject: - Fixed the "Block by Attribute Value" feature - Changed the "Block
 by Attribute Value" feature and the "Filter by Value" feature to only work on
 columns that are numeric or have a small number of distinct values
 (respectively)

---
 .../wqflask/static/new/javascript/show_trait.js    | 117 +++++++++++++++------
 .../templates/show_trait_transform_and_filter.html |  56 +++++++---
 2 files changed, 123 insertions(+), 50 deletions(-)

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 3df8784e..87c35984 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -568,14 +568,29 @@ create_value_dropdown = function(value) {
 populate_sample_attributes_values_dropdown = function() {
   var attribute_info, key, sample_attributes, selected_attribute, value, _i, _len, _ref, _ref1, _results;
   $('#attribute_values').empty();
-  sample_attributes = {};
-  attr_keys = Object.keys(js_data.attributes).sort();
-  for (i=0; i < attr_keys.length; i++) {
-    attribute_info = js_data.attributes[attr_keys[i]];
-    sample_attributes[attribute_info.name] = attribute_info.distinct_values;
-  }
-  selected_attribute = $('#exclude_menu').val().replace("_", " ");
-  _ref1 = sample_attributes[selected_attribute];
+  sample_attributes = [];
+
+  var attributes_as_list = Object.keys(js_data.attributes).map(function(key) {
+    return [key, js_data.attributes[key].name];
+  });
+
+  attributes_as_list.sort(function(first, second) {
+    if (second[1] > first[1]){
+      return -1
+    }
+    if (first[1] > second[1]){
+      return 1
+    }
+    return 0
+  });
+
+  for (i=0; i < attributes_as_list.length; i++) {
+    attribute_info = js_data.attributes[attributes_as_list[i][0]]
+    sample_attributes.push(attribute_info.distinct_values);
+  }
+
+  selected_attribute = $('#exclude_column').val()
+  _ref1 = sample_attributes[selected_attribute - 1];
   _results = [];
   for (_i = 0, _len = _ref1.length; _i < _len; _i++) {
     value = _ref1[_i];
@@ -590,23 +605,35 @@ if (Object.keys(js_data.attributes).length){
   populate_sample_attributes_values_dropdown();
 }
 
-$('#exclude_menu').change(populate_sample_attributes_values_dropdown);
+$('#exclude_column').change(populate_sample_attributes_values_dropdown);
 block_by_attribute_value = function() {
   var attribute_name, cell_class, exclude_by_value;
-  attribute_name = $('#exclude_menu').val();
+
+  let exclude_group = $('#exclude_by_attr_group').val();
+  let exclude_column = $('#exclude_column').val();
+
+  if (exclude_group === "other") {
+    var table_api = $('#samples_other').DataTable();
+  } else {
+    var table_api = $('#samples_primary').DataTable();
+  }
+
   exclude_by_value = $('#attribute_values').val();
-  cell_class = ".column_name-" + attribute_name;
-  return $(cell_class).each((function(_this) {
-    return function(index, element) {
-      var row;
-      if ($.trim($(element).text()) === exclude_by_value) {
-        row = $(element).parent('tr');
-        return $(row).find(".trait-value-input").val("x");
-      }
-    };
-  })(this));
+
+  let val_nodes = table_api.column(3).nodes().to$();
+  let exclude_val_nodes = table_api.column(attribute_start_pos + parseInt(exclude_column)).nodes().to$();
+
+  for (i = 0; i < exclude_val_nodes.length; i++) {
+    let this_col_value = exclude_val_nodes[i].childNodes[0].data;
+    let this_val_node = val_nodes[i].childNodes[0];
+
+    if (this_col_value == exclude_by_value){
+      this_val_node.value = "x";
+    }
+  }
 };
-$('#exclude_group').click(block_by_attribute_value);
+$('#exclude_by_attr').click(block_by_attribute_value);
+
 block_by_index = function() {
   var end_index, error, index, index_list, index_set, index_string, start_index, _i, _j, _k, _len, _len1, _ref;
   index_string = $('#remove_samples_field').val();
@@ -647,37 +674,57 @@ block_by_index = function() {
 
 filter_by_value = function() {
   let filter_logic = $('#filter_logic').val();
+  let filter_column = $('#filter_column').val();
   let filter_value = $('#filter_value').val();
+  let block_group = $('#filter_group').val();
 
-  block_group = $('#filter_group').val();
   if (block_group === "other") {
-    table_api = $('#samples_other').DataTable();
+    var table_api = $('#samples_other').DataTable();
   } else {
-    table_api = $('#samples_primary').DataTable();
+    var table_api = $('#samples_primary').DataTable();
   }
 
   let val_nodes = table_api.column(3).nodes().to$();
-  for (i = 0; i < val_nodes.length; i++) {
-    let this_node = val_nodes[i].childNodes[0];
-    if(!isNaN(this_node.value) && !isNaN(filter_value)) {
+  if (filter_column == "value"){
+    var filter_val_nodes = table_api.column(3).nodes().to$();
+  }
+  else if (filter_column == "stderr"){
+    var filter_val_nodes = table_api.column(5).nodes().to$();
+  }
+  else if (!isNaN(filter_column)){
+    var filter_val_nodes = table_api.column(attribute_start_pos + parseInt(filter_column)).nodes().to$();
+  }
+  else {
+    return false
+  }
+
+  for (i = 0; i < filter_val_nodes.length; i++) {
+    if (filter_column == "value" || filter_column == "stderr"){
+      var this_col_value = filter_val_nodes[i].childNodes[0].value;
+    } else {
+      var this_col_value = filter_val_nodes[i].childNodes[0].data;
+    }
+    let this_val_node = val_nodes[i].childNodes[0];
+
+    if(!isNaN(this_col_value) && !isNaN(filter_value)) {
       if (filter_logic == "greater_than"){
-        if (parseFloat(this_node.value) <= parseFloat(filter_value)){
-          this_node.value = "x";
+        if (parseFloat(this_col_value) <= parseFloat(filter_value)){
+          this_val_node.value = "x";
         }
       }
       else if (filter_logic == "less_than"){
-        if (parseFloat(this_node.value) >= parseFloat(filter_value)){
-          this_node.value = "x";
+        if (parseFloat(this_col_value) >= parseFloat(filter_value)){
+          this_val_node.value = "x";
         }
       }
       else if (filter_logic == "greater_or_equal"){
-        if (parseFloat(this_node.value) < parseFloat(filter_value)){
-          this_node.value = "x";
+        if (parseFloat(this_col_value) < parseFloat(filter_value)){
+          this_val_node.value = "x";
         }
       }
       else if (filter_logic == "less_or_equal"){
-        if (parseFloat(this_node.value) > parseFloat(filter_value)){
-          this_node.value = "x";
+        if (parseFloat(this_col_value) > parseFloat(filter_value)){
+          this_val_node.value = "x";
         }
       }
     }
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index 22c52d8c..d7eac378 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -20,8 +20,48 @@
     <div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
           Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
     </div>
+    {% if sample_groups[0].attributes %}
+    <div class="input-append block-div-2">
+        <label for="exclude_column">Block samples by group:</label>
+        <select id="exclude_column" size=1>
+          {% for attribute in sample_groups[0].attributes %}
+          {% if sample_groups[0].attributes[attribute].distinct_values|length <= 10 %}
+          <option value="{{ loop.index }}">
+              {{ sample_groups[0].attributes[attribute].name }}
+          </option>
+          {% endif %}
+          {% endfor %}
+        </select>
+        <select id="attribute_values" size=1>
+        </select>
+        <select id="exclude_by_attr_group" size="1">
+          <option value="primary">
+            {{ sample_group_types['samples_primary'] }}
+          </option>
+          <option value="other">
+            {{ sample_group_types['samples_other'] }}
+          </option>
+        </select>
+        <input type="button" id="exclude_by_attr" class="btn btn-danger" value="Block">
+    </div>
+    {% endif %}
     <div id="filterMenuSpan" class="input-append block-div-2">
-      <label for="filter_samples_field">Filter samples by value </label>
+      <label for="filter_samples_field">Filter samples by {% if not sample_groups[0].attributes %}value{% endif %} </label>
+      {% if sample_groups[0].attributes %}
+      <select id="filter_column">
+        <option value="value">Value</option>
+        {% if js_data.se_exists %}
+        <option value="stderr">SE</option>
+        {% endif %}
+        {% for attribute in sample_groups[0].attributes %}
+
+        <option value="{{ loop.index }}">
+          {{ sample_groups[0].attributes[attribute].name }}
+        </option>
+
+        {% endfor %}
+      </select>
+      {% endif %}
       <select id="filter_logic" size="1">
         <option value="greater_than">></option>
         <option value="less_than"><</option>
@@ -39,20 +79,6 @@
       </select>
       <input type="button" id="filter_by_value" class="btn btn-danger" value="Filter">
     </div>
-    {% if sample_groups[0].attributes %}
-    <div class="input-append block-div-2">
-        <label for="exclude_menu">Block samples by group:</label>
-        <select id="exclude_menu" size=1>
-          {% for attribute in sample_groups[0].attributes %}
-          <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}">
-              {{ sample_groups[0].attributes[attribute].name }}</option>
-          {% endfor %}
-        </select>
-        <select id="attribute_values" size=1>
-        </select>
-        <input type="button" id="exclude_group" class="btn" value="Block">
-    </div>
-    {% endif %}
     <div>
       <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">
-- 
cgit v1.2.3