From a224594125a88b75dcebc125e5e4b2394acedebb Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 15 Sep 2020 12:42:30 -0500
Subject: Added scroller to trait page and changed sample tables to use it

* wqflask/wqflask/templates/show_trait.html - Imported scroller (from
the Google cdn temporarily for testing) and activated it for the sample
tables, as well as disabled options that conflicted with it (like
paging: false)
---
 wqflask/wqflask/templates/show_trait.html | 35 +++++++++++++++----------------
 1 file changed, 17 insertions(+), 18 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 56df2049..fc65c5b1 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -150,6 +150,7 @@
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
+    <script type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.2/js/dataTables.scroller.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/noUiSlider/nouislider.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/get_covariates_from_collection.js"></script>
 
@@ -352,16 +353,15 @@
                   'order': [[1, "asc"]],
                   'sDom': "Ztr",
                   'autoWidth': true,
-                  'deferRender': true,
-                  'paging': false,
                   'orderClasses': true,
-                  'scrollY': "600px",
-                  'scrollCollapse': false,
-                  'processing': true,
-                  'language': {
-                    'loadingRecords': '&nbsp;',
-                    'processing': 'Loading...'
-                  }
+                  "scrollY": "50vh",
+                  'scroller':  true,
+                  'scrollCollapse': true
+                  // 'processing': true,
+                  // 'language': {
+                  //   'loadingRecords': '&nbsp;',
+                  //   'processing': 'Loading...'
+                  // }
                 } );
 
                 primary_table.on( 'order.dt search.dt draw.dt', function () {
@@ -502,16 +502,15 @@
                   'order': [[1, "asc"]],
                   'sDom': "Ztr",
                   'autoWidth': true,
-                  'deferRender': true,
-                  'paging': false,
                   'orderClasses': true,
-                  'scrollY': "600px",
-                  'scrollCollapse': false,
-                  'processing': true,
-                  'language': {
-                    'loadingRecords': '&nbsp;',
-                    'processing': 'Loading...'
-                  }
+                  "scrollY": "50vh",
+                  'scroller':  true,
+                  'scrollCollapse': true
+                  // 'processing': true,
+                  // 'language': {
+                  //   'loadingRecords': '&nbsp;',
+                  //   'processing': 'Loading...'
+                  // }
                 } );
 
                 $('#other_searchbox').on( 'keyup', function () {
-- 
cgit v1.2.3


From 07959c86e235072eaa46974ada5ea9c0432f49e7 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Sep 2020 13:54:11 -0500
Subject: Applied PEP8 and removed commented out code

---
 wqflask/wqflask/show_trait/SampleList.py | 67 +++++---------------------------
 1 file changed, 10 insertions(+), 57 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index ad78ebcc..10157558 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -1,21 +1,20 @@
 from __future__ import absolute_import, print_function, division
 
-from flask import Flask, g
-
-from base import webqtlCaseData
-from utility import webqtlUtil, Plot, Bunch
-from base.trait import GeneralTrait
+import itertools
 
 import numpy as np
-from scipy import stats
+from flask import Flask, g
 from pprint import pformat as pf
+from scipy import stats
 
-import simplejson as json
-
-import itertools
+from base import webqtlCaseData
+from base.trait import GeneralTrait
+from utility import logger
+from utility import webqtlUtil
+from utility import Plot
+from utility import Bunch
 
-import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = logger.getLogger(__name__ )
 
 class SampleList(object):
     def __init__(self,
@@ -35,8 +34,6 @@ class SampleList(object):
 
         self.get_attributes()
 
-        #self.sample_qnorm = get_transform_vals(self.dataset, this_trait)
-
         if self.this_trait and self.dataset:
             self.get_extra_attribute_values()
 
@@ -70,8 +67,6 @@ class SampleList(object):
 
             self.sample_list.append(sample)
 
-        #logger.debug("attribute vals are", pf(self.sample_attribute_values))
-
         self.do_outliers()
 
     def __repr__(self):
@@ -156,48 +151,6 @@ class SampleList(object):
 
         return any(sample.variance for sample in self.sample_list)
 
-# def get_transform_vals(dataset, trait):
-#     es = get_elasticsearch_connection(for_user=False)
-
-#     logger.info("DATASET NAME:", dataset.name)
-
-#     query = '{"bool": {"must": [{"match": {"name": "%s"}}, {"match": {"dataset": "%s"}}]}}' % (trait.name, dataset.name)
-
-#     es_body = {
-#           "query": {
-#             "bool": {
-#               "must": [
-#                 {
-#                   "match": {
-#                     "name": "%s" % (trait.name)
-#                   }
-#                 },
-#                 {
-#                   "match": {
-#                     "dataset": "%s" % (dataset.name)
-#                   }
-#                 }
-#               ]
-#             }
-#           }
-#     }
-
-#     response = es.search( index = "traits", doc_type = "trait", body = es_body )
-#     logger.info("THE RESPONSE:", response)
-#     results = response['hits']['hits']
-
-#     if len(results) > 0:
-#         samples = results[0]['_source']['samples']
-
-#         sample_dict = {}
-#         for sample in samples:
-#             sample_dict[sample['name']] = sample['qnorm']
-
-#         #logger.info("SAMPLE DICT:", sample_dict)
-#         return sample_dict
-#     else:
-#         return None
-
 def natural_sort_key(x):
     """Get expected results when using as a key for sort - ints or strings are sorted properly"""
 
-- 
cgit v1.2.3


From 64675d43272625464ef49e657dd9f61d8459e074 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Sep 2020 14:09:46 -0500
Subject: Changed se_exists to a property so the SampleList instance can
 include that when converted to a dict (which is needed to use it in the
 javascript)

* wqflask/wqflask/show_trait/SampleList.py - Directly set se_exists as a
property of SampleList instead of requiring a method be called; I could
have set self.se_exists by calling the se_exists method, but that would
have resulted in the convoluted line "self.se_exists = self.se_exists()"
and the se_exists method only consisted of one line anyways
---
 wqflask/wqflask/show_trait/SampleList.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 10157558..9e5be0e8 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -67,6 +67,7 @@ class SampleList(object):
 
             self.sample_list.append(sample)
 
+        self.se_exists = any(sample.variance for sample in self.sample_list)
         self.do_outliers()
 
     def __repr__(self):
@@ -146,11 +147,6 @@ class SampleList(object):
                     attribute_values[self.attributes[item.Id].name] = attribute_value
                 self.sample_attribute_values[sample_name] = attribute_values
 
-    def se_exists(self):
-        """Returns true if SE values exist for any samples, otherwise false"""
-
-        return any(sample.variance for sample in self.sample_list)
-
 def natural_sort_key(x):
     """Get expected results when using as a key for sort - ints or strings are sorted properly"""
 
-- 
cgit v1.2.3


From 870ddf6075f38c1ce5e7bf8f90742f06fe7d4805 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Sep 2020 14:15:46 -0500
Subject: Changed references to se_exists to just get it as a property of
 SampleList instead of calling the method

* wqflask/wqflask/show_trait/show_trait.py - see above
* wqflask/wqflask/templates/show_trait.html - see above + removed some
commented out code
---
 wqflask/wqflask/show_trait/show_trait.py  |  2 +-
 wqflask/wqflask/templates/show_trait.html | 20 +++++---------------
 2 files changed, 6 insertions(+), 16 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index f188fd9d..bc24098a 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -545,7 +545,7 @@ def get_table_widths(sample_groups, has_num_cases=False):
         stats_table_width = 450
 
     trait_table_width = 380
-    if sample_groups[0].se_exists():
+    if sample_groups[0].se_exists:
         trait_table_width += 80
     if has_num_cases:
         trait_table_width += 80
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index fc65c5b1..b7bffd79 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -211,7 +211,7 @@
 
                 //ZS: This variable is just created to get the column position of the first case attribute, since it's needed to set the row classes in createdRow for the DataTable
                 {% if sample_groups[0].attributes|length > 0 %}
-                {% if sample_groups[0].se_exists() %}
+                {% if sample_groups[0].se_exists %}
                 {% if has_num_cases %}
                 attribute_start_pos = 6
                 {% else %}
@@ -246,7 +246,7 @@
                     $('td', row).eq(2).addClass("column_name-Sample")
                     $('td', row).eq(3).addClass("column_name-Value")
                     $('td', row).eq(3).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% if sample_groups[0].se_exists() %}
+                    {% if sample_groups[0].se_exists %}
                     $('td', row).eq(4).attr("align", "center");
                     $('td', row).eq(4).attr("style", "padding-left: 2px; padding-right: 2px;");
                     $('td', row).eq(5).addClass("column_name-SE")
@@ -301,7 +301,7 @@
                           return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id) - 1] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id) - 1] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
                         }
                       }
-                    }{% if sample_groups[0].se_exists() %},
+                    }{% if sample_groups[0].se_exists %},
                     {
                       'bSortable': false,
                       'type': "natural",
@@ -357,11 +357,6 @@
                   "scrollY": "50vh",
                   'scroller':  true,
                   'scrollCollapse': true
-                  // 'processing': true,
-                  // 'language': {
-                  //   'loadingRecords': '&nbsp;',
-                  //   'processing': 'Loading...'
-                  // }
                 } );
 
                 primary_table.on( 'order.dt search.dt draw.dt', function () {
@@ -395,7 +390,7 @@
                     $('td', row).eq(2).addClass("column_name-Sample")
                     $('td', row).eq(3).addClass("column_name-Value")
                     $('td', row).eq(3).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% if sample_groups[1].se_exists() %}
+                    {% if sample_groups[1].se_exists %}
                     $('td', row).eq(4).attr("align", "center");
                     $('td', row).eq(4).attr("style", "padding-left: 2px; padding-right: 2px;");
                     $('td', row).eq(5).addClass("column_name-SE")
@@ -450,7 +445,7 @@
                           return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][1][parseInt(data.this_id)] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
                         }
                       }
-                    }{% if sample_groups[1].se_exists() %},
+                    }{% if sample_groups[1].se_exists %},
                     {
                       'bSortable': false,
                       'type': "natural",
@@ -506,11 +501,6 @@
                   "scrollY": "50vh",
                   'scroller':  true,
                   'scrollCollapse': true
-                  // 'processing': true,
-                  // 'language': {
-                  //   'loadingRecords': '&nbsp;',
-                  //   'processing': 'Loading...'
-                  // }
                 } );
 
                 $('#other_searchbox').on( 'keyup', function () {
-- 
cgit v1.2.3


From f376eaca55643972943fc6d313a3ca00b32d66ae Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Sep 2020 14:40:41 -0500
Subject: Made a bunch of changes to move trait page DataTables initialization
 to a separate file (initialize_show_trait_tables.js). The biggest
 complication was getting the order of attributes in the rows to sync with the
 order of atribute namees in the column headers. Previously this logic was all
 in the template. * wqflask/base/webqtlCaseData.py - added attribute
 first_attr_col as a very awkward solution to passing the column position into
 the column render function in situations where there are case attribute
 columns (which can be variable in number) *
 wqflask/wqflask/show_trait/show_trait.py - Replace "attribute_names" in
 js_data with "attributes" (which allows the JS access to more information)
 and also pass new se_exists and has_num_cases variables with js_data, so the
 javascript has access to whether or not those columns exist in the table *
 wqflask/wqflask/static/new/javascript/show_trait.js - Change case
 attribute-related logic to use js_data.attributes instead of
 js_data.attribute_names * wqflask/wqflask/templates/show_trait.html - Removed
 table initialization from template *
 wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - new
 file that initializes tables and reproduces what the template logic used to
 do with JS logic

---
 wqflask/base/webqtlCaseData.py                     |  11 +
 wqflask/wqflask/show_trait/show_trait.py           |  16 +-
 .../new/javascript/initialize_show_trait_tables.js | 222 ++++++++++++++++
 .../wqflask/static/new/javascript/show_trait.js    |  24 +-
 wqflask/wqflask/templates/show_trait.html          | 284 +--------------------
 5 files changed, 261 insertions(+), 296 deletions(-)
 create mode 100644 wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js

(limited to 'wqflask')

diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index 2844cedd..3cf2d80d 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -41,6 +41,8 @@ class webqtlCaseData:
         self.this_id = None   # Set a sane default (can't be just "id" cause that's a reserved word)
         self.outlier = None   # Not set to True/False until later
 
+        self.first_attr_col = self.get_first_attr_col()
+
     def __repr__(self):
         case_data_string = "<webqtlCaseData> "
         if self.value is not None:
@@ -79,3 +81,12 @@ class webqtlCaseData:
         if self.num_cases is not None:
             return "%s" % self.num_cases
         return "x"
+
+    def get_first_attr_col(self):
+        col_num = 4
+        if self.variance is not None:
+            col_num += 2
+        if self.num_cases is not None:
+            col_num += 1
+
+        return col_num
\ No newline at end of file
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index bc24098a..f1bd6f27 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -275,7 +275,9 @@ class ShowTrait(object):
                        data_scale = self.dataset.data_scale,
                        sample_group_types = self.sample_group_types,
                        sample_lists = sample_lists,
-                       attribute_names = self.sample_groups[0].attributes,
+                       se_exists = self.sample_groups[0].se_exists,
+                       has_num_cases = self.has_num_cases,
+                       attributes = self.sample_groups[0].attributes,
                        categorical_vars = ",".join(categorical_var_list),
                        num_values = self.num_values,
                        qnorm_values = self.qnorm_vals,
@@ -454,6 +456,7 @@ class ShowTrait(object):
         self.primary_sample_names = primary_sample_names
         self.dataset.group.allsamples = all_samples_ordered
 
+
 def quantile_normalize_vals(sample_groups):
     def normf(trait_vals):
         ranked_vals = ss.rankdata(trait_vals)
@@ -492,6 +495,7 @@ def quantile_normalize_vals(sample_groups):
 
     return qnorm_by_group
 
+
 def get_z_scores(sample_groups):
     zscore_by_group = []
     for sample_type in sample_groups:
@@ -516,6 +520,7 @@ def get_z_scores(sample_groups):
 
     return zscore_by_group
 
+
 def get_nearest_marker(this_trait, this_db):
     this_chr = this_trait.locus_chr
     logger.debug("this_chr:", this_chr)
@@ -539,6 +544,7 @@ def get_nearest_marker(this_trait, this_db):
     else:
         return result[0][0]
 
+
 def get_table_widths(sample_groups, has_num_cases=False):
     stats_table_width = 250
     if len(sample_groups) > 1:
@@ -555,6 +561,7 @@ def get_table_widths(sample_groups, has_num_cases=False):
 
     return stats_table_width, trait_table_width
 
+
 def has_num_cases(this_trait):
     has_n = False
     if this_trait.dataset.type != "ProbeSet" and this_trait.dataset.type != "Geno":
@@ -565,6 +572,7 @@ def has_num_cases(this_trait):
 
     return has_n
 
+
 def get_trait_units(this_trait):
     unit_type = ""
     inside_brackets = False
@@ -584,6 +592,7 @@ def get_trait_units(this_trait):
 
     return unit_type
 
+
 def check_if_attr_exists(the_trait, id_type):
     if hasattr(the_trait, id_type):
         if getattr(the_trait, id_type) == None or getattr(the_trait, id_type) == "":
@@ -593,6 +602,7 @@ def check_if_attr_exists(the_trait, id_type):
     else:
         return False
 
+
 def get_ncbi_summary(this_trait):
     if check_if_attr_exists(this_trait, 'geneid'):
         #ZS: Need to switch this try/except to something that checks the output later
@@ -605,6 +615,7 @@ def get_ncbi_summary(this_trait):
     else:
         return None
 
+
 def get_categorical_variables(this_trait, sample_list):
     categorical_var_list = []
 
@@ -623,6 +634,7 @@ def get_categorical_variables(this_trait, sample_list):
 
     return categorical_var_list
 
+
 def get_genotype_scales(genofiles):
     geno_scales = {}
     if type(genofiles) is list:
@@ -634,6 +646,7 @@ def get_genotype_scales(genofiles):
 
     return geno_scales
 
+
 def get_scales_from_genofile(file_location):
     geno_path = locate_ignore_error(file_location, 'genotype')
 
@@ -686,6 +699,7 @@ def get_scales_from_genofile(file_location):
                 if i > first_marker_line + 10:
                     break
 
+
     #ZS: This assumes that both won't be all zero, since if that's the case mapping shouldn't be an option to begin with
     if mb_all_zero:
         return [["morgan", "cM"]]
diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
new file mode 100644
index 00000000..41ddc088
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -0,0 +1,222 @@
+// ZS: This file initializes the tables for the show_trait page
+
+// ZS: This variable is just created to get the column position of the first case attribute (if case attributes exist), since it's needed to set the row classes in createdRow for the DataTable
+attribute_start_pos = 3
+if (js_data.se_exists === "true") {
+  attribute_start_pos += 2
+}
+if (js_data.has_num_cases === "true") {
+  attribute_start_post += 1
+}
+
+build_columns = function() {
+  let column_list = [
+    {
+      'data': null,
+      'orderDataType': "dom-checkbox",
+      'searchable' : false,
+      'render': function(data, type, row, meta) {
+      return '<input type="checkbox" name="searchResult" style="min-height: 20px;" class="checkbox edit_sample_checkbox" value="">'
+      }
+    },
+    {
+      'title': "ID",
+      'type': "natural",
+      'searchable' : false,
+      'data': "this_id"
+    },
+    {
+      'title': "Sample",
+      'type': "natural",
+      'data': null,
+      'render': function(data, type, row, meta) {
+      return '<span class="edit_sample_sample_name">' + data.name + '</span>'
+      }
+    },
+    {
+      'title': "<div style='text-align: right;'>Value</div>",
+      'orderDataType': "dom-input",
+      'type': "cust-txt",
+      'data': null,
+      'render': function(data, type, row, meta) {
+        if (data.value == null) {
+            return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=6 maxlength=6>'
+        } else {
+            return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id) - 1] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id) - 1] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
+        }
+      }
+    }
+  ];
+
+  if (js_data.se_exists === "true") {
+    column_list.push(
+      {
+        'bSortable': false,
+        'type': "natural",
+        'data': null,
+        'searchable' : false,
+        'render': function(data, type, row, meta) {
+        return '±'
+        }
+      },
+      {
+        'title': "<div style='text-align: right;'>SE</div>",
+        'orderDataType': "dom-input",
+        'type': "cust-txt",
+        'data': null,
+        'render': function(data, type, row, meta) {
+          if (data.variance == null) {
+              return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="x" size=6 maxlength=6>'
+          } else {
+              return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>'
+          }
+        }
+      }
+    );
+  }
+
+  if (js_data.has_num_cases === "true") {
+    column_list.push(
+      {
+        'title': "<div style='text-align: right;'>N</div>",
+        'orderDataType': "dom-input",
+        'type': "cust-txt",
+        'data': null,
+        'render': function(data, type, row, meta) {
+          if (data.num_cases == null || data.num_cases == undefined) {
+              return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>'
+          } else {
+              return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>'
+          }
+        }
+      }
+    );
+  }
+
+  attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].name > js_data.attributes[b].name) ? 1 : -1)
+  for (i = 0; i < attr_keys.length; i++){
+    column_list.push(
+      {
+        'title': "<div style='text-align: " + js_data.attributes[attr_keys[i]].alignment + "'>" + js_data.attributes[attr_keys[i]].name + "</div>",
+        'type': "natural",
+        'data': null,
+        'render': function(data, type, row, meta) {
+          attr_name = Object.keys(data.extra_attributes).sort((a, b) => (a > b) ? 1 : -1)[meta.col - data.first_attr_col]
+          if (attr_name != null && attr_name != undefined){
+              return data.extra_attributes[attr_name]
+          } else {
+              return ""
+          }
+        }
+      }
+    )
+  }
+
+  return column_list
+}
+
+var primary_table = $('#samples_primary').DataTable( {
+    'initComplete': function(settings, json) {
+    $('.edit_sample_value').change(function() {
+        edit_data_change();
+    });
+    },
+    'createdRow': function ( row, data, index ) {
+      $(row).attr('id', "Primary_" + data.this_id)
+      $(row).addClass("value_se");
+      if (data.outlier) {
+        $(row).addClass("outlier");
+      }
+      $('td', row).eq(1).addClass("column_name-Index")
+      $('td', row).eq(2).addClass("column_name-Sample")
+      $('td', row).eq(3).addClass("column_name-Value")
+      if (js_data.se_exists === "true") {
+        $('td', row).eq(5).addClass("column_name-SE")
+        if (js_data.has_num_cases === "true") {
+          $('td', row).eq(6).addClass("column_name-num_cases")
+        } else {
+          if (js_data.has_num_cases === "true") {
+            $('td', row).eq(4).addClass("column_name-num_cases")
+          }
+        }
+      } else {
+        if (js_data.has_num_cases === "true") {
+          $('td', row).eq(4).addClass("column_name-num_cases")
+        }
+      }
+
+      sorted_key_list = Object.keys(js_data.attributes).sort()
+      for (i=0; i < sorted_key_list.length; i++) {
+        $('td', row).eq(attribute_start_pos + i).addClass("column_name-" + js_data.attributes[sorted_key_list[i]].name)
+        $('td', row).eq(attribute_start_pos + i).attr("style", "text-align: " + js_data.attributes[sorted_key_list[i]].alignment + "; padding-top: 2px; padding-bottom: 0px;")
+      }
+    },
+    'data': js_data['sample_lists'][0],
+    'columns': build_columns(),
+    'order': [[1, "asc"]],
+    'sDom': "Ztr",
+    'autoWidth': true,
+    'orderClasses': true,
+    "scrollY": "50vh",
+    'scroller':  true,
+    'scrollCollapse': true
+} );
+
+primary_table.on( 'order.dt search.dt draw.dt', function () {
+    primary_table.column(1, {search:'applied', order:'applied'}).nodes().each( function (cell, i) {
+    cell.innerHTML = i+1;
+    } );
+} ).draw();
+
+$('#primary_searchbox').on( 'keyup', function () {
+    primary_table.search($(this).val()).draw();
+} );
+
+if (js_data.sample_lists.length > 1){
+  var other_table = $('#samples_other').DataTable( {
+      'initComplete': function(settings, json) {
+      $('.edit_sample_value').change(function() {
+          edit_data_change();
+      });
+      },
+      'createdRow': function ( row, data, index ) {
+        $(row).attr('id', "Primary_" + data.this_id)
+        $(row).addClass("value_se");
+        if (data.outlier) {
+          $(row).addClass("outlier");
+        }
+        $('td', row).eq(1).addClass("column_name-Index")
+        $('td', row).eq(2).addClass("column_name-Sample")
+        $('td', row).eq(3).addClass("column_name-Value")
+        if (js_data.se_exists === "true") {
+          $('td', row).eq(5).addClass("column_name-SE")
+          if (js_data.has_num_cases === "true") {
+            $('td', row).eq(6).addClass("column_name-num_cases")
+          } else {
+            if (js_data.has_num_cases === "true") {
+              $('td', row).eq(4).addClass("column_name-num_cases")
+            }
+          }
+        } else {
+          if (js_data.has_num_cases === "true") {
+            $('td', row).eq(4).addClass("column_name-num_cases")
+          }
+        }
+
+        sorted_key_list = Object.keys(js_data.attributes).sort()
+        for (i=0; i < sorted_key_list.length; i++) {
+          $('td', row).eq(attribute_start_pos + i).addClass("column_name-" + js_data.attributes[sorted_key_list[i]].name)
+          $('td', row).eq(attribute_start_pos + i).attr("style", "text-align: " + js_data.attributes[sorted_key_list[i]].alignment + "; padding-top: 2px; padding-bottom: 0px;")
+        }
+      },
+      'data': js_data['sample_lists'][1],
+      'columns': build_columns(),
+      'order': [[1, "asc"]],
+      'sDom': "Ztr",
+      'autoWidth': true,
+      'orderClasses': true,
+      "scrollY": "50vh",
+      'scroller':  true,
+      'scrollCollapse': true
+  } );
+}
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index c0784073..0b5ae6f9 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -538,10 +538,9 @@ 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 = {};
-  _ref = js_data.attribute_names;
-  for (key in _ref) {
-    if (!__hasProp.call(_ref, key)) continue;
-    attribute_info = _ref[key];
+  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 = $('#exclude_menu').val().replace("_", " ");
@@ -549,13 +548,15 @@ populate_sample_attributes_values_dropdown = function() {
   _results = [];
   for (_i = 0, _len = _ref1.length; _i < _len; _i++) {
     value = _ref1[_i];
-    _results.push($(create_value_dropdown(value)).appendTo($('#attribute_values')));
+    if (value != ""){
+      _results.push($(create_value_dropdown(value)).appendTo($('#attribute_values')));
+    }
   }
   return _results;
 };
-if (Object.keys(js_data.attribute_names).length > 0) {
-  populate_sample_attributes_values_dropdown();
-}
+
+populate_sample_attributes_values_dropdown();
+
 $('#exclude_menu').change(populate_sample_attributes_values_dropdown);
 block_by_attribute_value = function() {
   var attribute_name, cell_class, exclude_by_value;
@@ -859,10 +860,9 @@ get_sample_table_data = function(table_name) {
       if ($(element).find('.edit_sample_num_cases').length > 0) {
         row_data.num_cases = $(element).find('.edit_sample_num_cases').val();
       }
-      _ref = js_data.attribute_names;
-      for (key in _ref) {
-        if (!__hasProp.call(_ref, key)) continue;
-        attribute_info = _ref[key];
+      attr_keys = Object.keys(js_data.attributes).sort()
+      for (i=0; i < attr_keys.length; i++) {
+        attribute_info = js_data.attributes[attr_keys[i]];
         row_data[attribute_info.name] = $.trim($(element).find('.column_name-' + attribute_info.name.replace(" ", "_").replace("/", "\\/")).text());
       }
       return samples.push(row_data);
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index b7bffd79..0a79ad48 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -153,6 +153,7 @@
     <script type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.2/js/dataTables.scroller.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/noUiSlider/nouislider.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/get_covariates_from_collection.js"></script>
+    <script type="text/javascript" src="/static/new/javascript/initialize_show_trait_tables.js"></script>
 
     <script type="text/javascript" charset="utf-8">
 
@@ -209,156 +210,6 @@
                    }
                 });
 
-                //ZS: This variable is just created to get the column position of the first case attribute, since it's needed to set the row classes in createdRow for the DataTable
-                {% if sample_groups[0].attributes|length > 0 %}
-                {% if sample_groups[0].se_exists %}
-                {% if has_num_cases %}
-                attribute_start_pos = 6
-                {% else %}
-                attribute_start_pos = 5
-                {% endif %}
-                {% else %}
-                {% if has_num_cases %}
-                attribute_start_pos = 4
-                {% else %}
-                attribute_start_pos = 3
-                {% endif %}
-                {% endif %}
-                {% endif %}
-
-                var primary_table = $('#samples_primary').DataTable( {
-                  'initComplete': function(settings, json) {
-                    $('.edit_sample_value').change(function() {
-                      edit_data_change();
-                    });
-                  },
-                  'createdRow': function ( row, data, index ) {
-                    $(row).attr('id', "Primary_" + data.this_id)
-                    $(row).addClass("value_se");
-                    if (data.outlier) {
-                      $(row).addClass("outlier");
-                    }
-                    $('td', row).eq(0).attr("align", "center");
-                    $('td', row).eq(0).attr("style", "padding: 2px 0px 0px 2px;");
-                    $('td', row).eq(1).addClass("column_name-Index")
-                    $('td', row).eq(1).attr("align", "right");
-                    $('td', row).eq(1).attr("style", "padding: 2px 4px 0px 2px;");
-                    $('td', row).eq(2).addClass("column_name-Sample")
-                    $('td', row).eq(3).addClass("column_name-Value")
-                    $('td', row).eq(3).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% if sample_groups[0].se_exists %}
-                    $('td', row).eq(4).attr("align", "center");
-                    $('td', row).eq(4).attr("style", "padding-left: 2px; padding-right: 2px;");
-                    $('td', row).eq(5).addClass("column_name-SE")
-                    $('td', row).eq(5).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% if has_num_cases %}
-                    $('td', row).eq(6).addClass("column_name-num_cases")
-                    $('td', row).eq(6).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% endif %} {% else %} {% if has_num_cases %}
-                    $('td', row).eq(4).addClass("column_name-num_cases")
-                    $('td', row).eq(4).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% endif %} {% endif %}
-                    {% if sample_groups[0].attributes|length > 0 %}
-                    {% for attribute in sample_groups[0].attributes|sort() %}
-                    $('td', row).eq(attribute_start_pos + {{ loop.index }}).addClass("column_name-{{ sample_groups[0].attributes[attribute].name }}")
-                    $('td', row).eq(attribute_start_pos + {{ loop.index }}).attr("style", "text-align: {{ sample_groups[0].attributes[attribute].alignment }}; padding-top: 2px; padding-bottom: 0px;")
-                    {% endfor %}
-                    {% endif %}
-                  },
-                  'data': js_data['sample_lists'][0],
-                  'columns': [
-                    {
-                      'data': null,
-                      'orderDataType': "dom-checkbox",
-                      'searchable' : false,
-                      'render': function(data, type, row, meta) {
-                        return '<input type="checkbox" name="searchResult" style="min-height: 20px;" class="checkbox edit_sample_checkbox" value="">'
-                      }
-                    },
-                    {
-                      'title': "ID",
-                      'type': "natural",
-                      'searchable' : false,
-                      'data': "this_id"
-                    },
-                    {
-                      'title': "Sample",
-                      'type': "natural",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        return '<span class="edit_sample_sample_name">' + data.name + '</span>'
-                      }
-                    },
-                    {
-                      'title': "<div style='text-align: right;'>Value</div>",
-                      'orderDataType': "dom-input",
-                      'type': "cust-txt",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        if (data.value == null) {
-                          return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=6 maxlength=6>'
-                        } else {
-                          return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id) - 1] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id) - 1] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
-                        }
-                      }
-                    }{% if sample_groups[0].se_exists %},
-                    {
-                      'bSortable': false,
-                      'type': "natural",
-                      'data': null,
-                      'searchable' : false,
-                      'render': function(data, type, row, meta) {
-                        return '±'
-                      }
-                    },
-                    {
-                      'title': "<div style='text-align: right;'>SE</div>",
-                      'orderDataType': "dom-input",
-                      'type': "cust-txt",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        if (data.variance == null) {
-                          return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="x" size=6 maxlength=6>'
-                        } else {
-                          return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>'
-                        }
-                      }
-                    }{% endif %}{% if has_num_cases %},
-                    {
-                      'title': "<div style='text-align: right;'>N</div>",
-                      'orderDataType': "dom-input",
-                      'type': "cust-txt",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        if (data.num_cases == null || data.num_cases == undefined) {
-                          return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>'
-                        } else {
-                          return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>'
-                        }
-                      }
-                    }{% endif %}{% if sample_groups[0].attributes|length > 0 %}{% for attribute in sample_groups[0].attributes|sort() %},
-                    {
-                      'title': "<div style='text-align: {{ sample_groups[0].attributes[attribute].alignment }}'>{{ sample_groups[0].attributes[attribute].name }}</div>",
-                      'type': "natural",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        if (data.extra_attributes['{{ sample_groups[0].attributes[attribute].name }}'] != null && data.extra_attributes['{{ sample_groups[0].attributes[attribute].name }}'] != undefined){
-                          return data.extra_attributes['{{ sample_groups[0].attributes[attribute].name }}']
-                        } else {
-                          return ""
-                        }
-                      }
-                    }{% endfor %}{% endif %}
-                  ],
-                  'order': [[1, "asc"]],
-                  'sDom': "Ztr",
-                  'autoWidth': true,
-                  'orderClasses': true,
-                  "scrollY": "50vh",
-                  'scroller':  true,
-                  'scrollCollapse': true
-                } );
-
                 primary_table.on( 'order.dt search.dt draw.dt', function () {
                   primary_table.column(1, {search:'applied', order:'applied'}).nodes().each( function (cell, i) {
                     cell.innerHTML = i+1;
@@ -370,139 +221,6 @@
                 } );
 
                 {% if sample_groups|length != 1 %}
-                var other_table = $('#samples_other').DataTable( {
-                  'initComplete': function(settings, json) {
-                    $('.edit_sample_value').change(function() {
-                      edit_data_change();
-                    });
-                  },
-                  'createdRow': function ( row, data, index ) {
-                    $(row).attr('id', "Other_" + data.this_id)
-                    $(row).addClass("value_se");
-                    if (data.outlier) {
-                      $(row).addClass("outlier");
-                    }
-                    $('td', row).eq(0).attr("align", "center");
-                    $('td', row).eq(0).attr("style", "padding: 2px 0px 0px 2px;");
-                    $('td', row).eq(1).addClass("column_name-Index")
-                    $('td', row).eq(1).attr("align", "right");
-                    $('td', row).eq(1).attr("style", "padding: 2px 4px 0px 2px;");
-                    $('td', row).eq(2).addClass("column_name-Sample")
-                    $('td', row).eq(3).addClass("column_name-Value")
-                    $('td', row).eq(3).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% if sample_groups[1].se_exists %}
-                    $('td', row).eq(4).attr("align", "center");
-                    $('td', row).eq(4).attr("style", "padding-left: 2px; padding-right: 2px;");
-                    $('td', row).eq(5).addClass("column_name-SE")
-                    $('td', row).eq(5).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% if has_num_cases %}
-                    $('td', row).eq(6).addClass("column_name-num_cases")
-                    $('td', row).eq(6).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% endif %} {% else %} {% if has_num_cases %}
-                    $('td', row).eq(4).addClass("column_name-num_cases")
-                    $('td', row).eq(4).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% endif %} {% endif %}
-                    {% if sample_groups[1].attributes|length > 0 %}
-                    {% for attribute in sample_groups[1].attributes|sort() %}
-                    $('td', row).eq(attribute_start_pos + {{ loop.index }}).addClass("column_name-{{ sample_groups[1].attributes[attribute].name }}")
-                    $('td', row).eq(attribute_start_pos + {{ loop.index }}).attr("style", "text-align: {{ sample_groups[1].attributes[attribute].alignment }}; padding-top: 2px; padding-bottom: 0px;")
-                    {% endfor %}
-                    {% endif %}
-                  },
-                  'data': js_data['sample_lists'][1],
-                  'columns': [
-                    {
-                      'data': null,
-                      'orderDataType': "dom-checkbox",
-                      'searchable' : false,
-                      'render': function(data, type, row, meta) {
-                        return '<input type="checkbox" name="searchResult" style="min-height: 20px;" class="checkbox edit_sample_checkbox" value="">'
-                      }
-                    },
-                    {
-                      'title': "ID",
-                      'type': "natural",
-                      'data': "this_id",
-                      'searchable' : false
-                    },
-                    {
-                      'title': "Sample",
-                      'type': "natural",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        return '<span class="edit_sample_sample_name">' + data.name + '</span>'
-                      }
-                    },
-                    {
-                      'title': "<div style='text-align: right;'>Value</div>",
-                      'orderDataType': "dom-input",
-                      'type': "cust-txt",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        if (data.value == null) {
-                          return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=6 maxlength=6>'
-                        } else {
-                          return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][1][parseInt(data.this_id)] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
-                        }
-                      }
-                    }{% if sample_groups[1].se_exists %},
-                    {
-                      'bSortable': false,
-                      'type': "natural",
-                      'data': null,
-                      'searchable' : false,
-                      'render': function(data, type, row, meta) {
-                        return '±'
-                      }
-                    },
-                    {
-                      'title': "<div style='text-align: right;'>SE</div>",
-                      'orderDataType': "dom-input",
-                      'type': "cust-txt",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        if (data.variance == null) {
-                          return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="x" size=6 maxlength=6>'
-                        } else {
-                          return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>'
-                        }
-                      }
-                    }{% endif %}{% if has_num_cases %},
-                    {
-                      'title': "<div style='text-align: right;'>N</div>",
-                      'orderDataType': "dom-input",
-                      'type': "cust-txt",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        if (data.num_cases == null) {
-                          return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>'
-                        } else {
-                          return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>'
-                        }
-                      }
-                    }{% endif %}{% if sample_groups[1].attributes|length > 0 %}{% for attribute in sample_groups[1].attributes|sort() %},
-                    {
-                      'title': "<div style='text-align: {{ sample_groups[1].attributes[attribute].alignment }}'>{{ sample_groups[1].attributes[attribute].name }}</div>",
-                      'type': "natural",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        if (data.extra_attributes['{{ sample_groups[1].attributes[attribute].name }}'] != null && data.extra_attributes['{{ sample_groups[1].attributes[attribute].name }}'] != undefined){
-                          return data.extra_attributes['{{ sample_groups[1].attributes[attribute].name }}']
-                        } else {
-                          return ""
-                        }
-                      }
-                    }{% endfor %}{% endif %}
-                  ],
-                  'order': [[1, "asc"]],
-                  'sDom': "Ztr",
-                  'autoWidth': true,
-                  'orderClasses': true,
-                  "scrollY": "50vh",
-                  'scroller':  true,
-                  'scrollCollapse': true
-                } );
-
                 $('#other_searchbox').on( 'keyup', function () {
                   other_table.search($(this).val()).draw();
                 } );
-- 
cgit v1.2.3


From a7a9394b517d551a9ba8f77bd4adf1cc3e0ae46f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Sep 2020 14:51:06 -0500
Subject: Made some style changes with whitespace/line-breaks

---
 wqflask/wqflask/show_trait/SampleList.py | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 9e5be0e8..356db7bc 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -40,17 +40,16 @@ class SampleList(object):
         for counter, sample_name in enumerate(sample_names, 1):
             sample_name = sample_name.replace("_2nd_", "")
 
-            if type(self.this_trait) is list: #ZS: self.this_trait will be a list if it is a Temp trait
+            if type(self.this_trait) is list: # ZS: self.this_trait will be a list if it is a Temp trait
                 if counter <= len(self.this_trait) and str(self.this_trait[counter-1]).upper() != 'X':
                     sample = webqtlCaseData.webqtlCaseData(name=sample_name, value=float(self.this_trait[counter-1]))
                 else:
                     sample = webqtlCaseData.webqtlCaseData(name=sample_name)
             else:
-                #ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table)
+                # ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table)
                 try:
                     sample = self.this_trait.data[sample_name]
                 except KeyError:
-                    #logger.debug("No sample %s, let's create it now" % sample_name)
                     sample = webqtlCaseData.webqtlCaseData(name=sample_name)
 
             sample.extra_info = {}
@@ -60,10 +59,9 @@ class SampleList(object):
 
             sample.this_id = str(counter)
 
-            #### For extra attribute columns; currently only used by several datasets - Zach
+            # ZS: For extra attribute columns; currently only used by several datasets
             if self.sample_attribute_values:
                 sample.extra_attributes = self.sample_attribute_values.get(sample_name, {})
-                #logger.debug("sample.extra_attributes is", pf(sample.extra_attributes))
 
             self.sample_list.append(sample)
 
@@ -100,7 +98,6 @@ class SampleList(object):
         self.attributes = {}
         for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)):
             key, name = attr
-            #logger.debug("radish: %s - %s" % (key, name))
             self.attributes[key] = Bunch()
             self.attributes[key].name = name
             self.attributes[key].distinct_values = [item.Value for item in values]
@@ -137,8 +134,8 @@ class SampleList(object):
                 for item in items:
                     attribute_value = item.Value
 
-                    #ZS: If it's an int, turn it into one for sorting
-                    #(for example, 101 would be lower than 80 if they're strings instead of ints)
+                    # ZS: If it's an int, turn it into one for sorting
+                    # (for example, 101 would be lower than 80 if they're strings instead of ints)
                     try:
                         attribute_value = int(attribute_value)
                     except ValueError:
-- 
cgit v1.2.3


From 194a53126f636ad845ca2423f3928170cdfb6a2f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 22 Sep 2020 14:43:48 -0500
Subject: Changed JS on trait page that updates basic stats and graphs/figures
 to use the DataTables API to pull sample values

* wqflask/wqflask/static/new/javascript/show_trait.js - Changed the way
sample name/val/var are pulled from the table to instead use DataTables'
API + removed an unused event listener
* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
- added "var" before a defined variable for consistency
---
 .../new/javascript/initialize_show_trait_tables.js |  6 +--
 .../wqflask/static/new/javascript/show_trait.js    | 57 ++++++++++++----------
 2 files changed, 33 insertions(+), 30 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
index 41ddc088..53d5b3f7 100644
--- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
+++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -1,12 +1,12 @@
 // ZS: This file initializes the tables for the show_trait page
 
 // ZS: This variable is just created to get the column position of the first case attribute (if case attributes exist), since it's needed to set the row classes in createdRow for the DataTable
-attribute_start_pos = 3
+var attribute_start_pos = 3;
 if (js_data.se_exists === "true") {
-  attribute_start_pos += 2
+  attribute_start_pos += 2;
 }
 if (js_data.has_num_cases === "true") {
-  attribute_start_post += 1
+  attribute_start_post += 1;
 }
 
 build_columns = function() {
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 0b5ae6f9..40db07d7 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -440,38 +440,40 @@ edit_data_change = function() {
     samples_other: {},
     samples_all: {}
   };
+
   tables = ['samples_primary', 'samples_other'];
   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];
-      name = $(row).find('.edit_sample_sample_name').html();
-      name = $.trim(name);
-      real_value = $(row).find('.edit_sample_value').val();
-      checkbox = $(row).find(".edit_sample_checkbox");
-      if (is_number(real_value) && real_value !== "") {
-        real_value = parseFloat(real_value);
-        sample_sets[table].add_value(real_value);
-        real_variance = $(row).find('.edit_sample_se').val();
-        if (is_number(real_variance)) {
-          real_variance = parseFloat(real_variance);
-        } else {
-          real_variance = null;
-        }
-        real_dict = {
-          value: real_value,
-          variance: real_variance
-        };
-        root.selected_samples[table][name] = real_dict;
-        if (!(name in already_seen)) {
-          sample_sets['samples_all'].add_value(real_value);
-          root.selected_samples['samples_all'][name] = real_dict;
-          already_seen[name] = true;
+    if ($('#' + table).length){
+      table_api = $('#' + table).DataTable();
+      table_api.rows().eq(0).each( function ( index ) {
+        var row = primary_table.row( index );
+        sample_val = primary_table.cell(index, 3).nodes().to$().find('.edit_sample_value').val()
+        sample_name = $.trim(primary_table.cell(index, 2).nodes().to$().find('.edit_sample_sample_name').html())
+        if (is_number(sample_val) && sample_val !== "") {
+          sample_val = parseFloat(sample_val);
+          sample_sets[table].add_value(sample_val);
+          sample_var = primary_table.cell(index, 5).nodes().to$().find('.edit_sample_se').val()
+          if (is_number(sample_var)) {
+            sample_var = parseFloat(sample_var)
+          } else {
+            sample_var = null;
+          }
+          sample_dict = {
+            value: sample_val,
+            variance: sample_var
+          }
+          root.selected_samples[table][sample_name] = sample_dict;
+          if (!(sample_name in already_seen)) {
+            sample_sets['samples_all'].add_value(sample_val);
+            root.selected_samples['samples_all'][sample_name] = sample_dict;
+            already_seen[sample_name] = true;
+          }
         }
-      }
+      } );
     }
   }
+
   update_stat_values(sample_sets);
 
   if ($('#histogram').hasClass('js-plotly-plot')){
@@ -1447,7 +1449,8 @@ $('.stats_panel').click(function() {
     edit_data_change();
   }
 });
-$('#edit_sample_lists').change(edit_data_change);
+
+$('.edit_sample_value').change(edit_data_change);
 $('#block_by_index').click(edit_data_change);
 $('#exclude_group').click(edit_data_change);
 $('#block_outliers').click(edit_data_change);
-- 
cgit v1.2.3


From 0aa2d5271b703fd37fb9c6a7511ecfe551268d36 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 24 Sep 2020 23:39:26 -0500
Subject: Changed logic that defines the primary/other samplelists to be much
 more efficient

* wqflask/wqflask/show_trait/show_trait.py - Add an "if" statement to
avoid unnecessarily running some code and changed a list to a set for
the purposes of searching if it contains an element
---
 wqflask/wqflask/show_trait/show_trait.py | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index f1bd6f27..30b03e66 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -43,8 +43,6 @@ logger = getLogger(__name__ )
 class ShowTrait(object):
 
     def __init__(self, kw):
-        logger.debug("in ShowTrait, kw are:", kw)
-
         if 'trait_id' in kw and kw['dataset'] != "Temp":
             self.temp_trait = False
             self.trait_id = kw['trait_id']
@@ -152,6 +150,7 @@ class ShowTrait(object):
                 #self.nearest_marker1 = ""
                 #self.nearest_marker2 = ""
 
+
         self.make_sample_lists()
 
         self.qnorm_vals = quantile_normalize_vals(self.sample_groups)
@@ -397,6 +396,7 @@ class ShowTrait(object):
                                           return_results_menu_selected = return_results_menu_selected,)
 
     def make_sample_lists(self):
+
         all_samples_ordered = self.dataset.group.all_samples_ordered()
         
         parent_f1_samples = []
@@ -405,13 +405,18 @@ class ShowTrait(object):
 
         primary_sample_names = list(all_samples_ordered)
 
+
         if not self.temp_trait:
             other_sample_names = []
-            for sample in self.this_trait.data.keys():
-                if (self.this_trait.data[sample].name2 in primary_sample_names) and (self.this_trait.data[sample].name not in primary_sample_names):
-                    primary_sample_names.append(self.this_trait.data[sample].name)
-                    primary_sample_names.remove(self.this_trait.data[sample].name2)
-                elif sample not in all_samples_ordered:
+
+            for sample in self.this_trait.data:
+                if self.this_trait.data[sample].name2 != self.this_trait.data[sample].name:
+                    if (self.this_trait.data[sample].name2 in primary_sample_names) and (self.this_trait.data[sample].name not in primary_sample_names):
+                        primary_sample_names.append(self.this_trait.data[sample].name)
+                        primary_sample_names.remove(self.this_trait.data[sample].name2)
+
+                all_samples_set = set(all_samples_ordered)
+                if sample not in all_samples_set:
                     all_samples_ordered.append(sample)
                     other_sample_names.append(sample)
 
@@ -424,6 +429,7 @@ class ShowTrait(object):
                 primary_header = "%s Only" % (self.dataset.group.name)
             else:
                 primary_header = "Samples"
+
             primary_samples = SampleList(dataset = self.dataset,
                                             sample_names=primary_sample_names,
                                             this_trait=self.this_trait,
@@ -523,9 +529,7 @@ def get_z_scores(sample_groups):
 
 def get_nearest_marker(this_trait, this_db):
     this_chr = this_trait.locus_chr
-    logger.debug("this_chr:", this_chr)
     this_mb = this_trait.locus_mb
-    logger.debug("this_mb:", this_mb)
     #One option is to take flanking markers, another is to take the two (or one) closest
     query = """SELECT Geno.Name
                FROM Geno, GenoXRef, GenoFreeze
@@ -536,7 +540,6 @@ def get_nearest_marker(this_trait, this_db):
                ORDER BY ABS( Geno.Mb - {}) LIMIT 1""".format(this_chr, this_db.group.name+"Geno", this_mb)
     logger.sql(query)
     result = g.db.execute(query).fetchall()
-    logger.debug("result:", result)
 
     if result == []:
         return ""
-- 
cgit v1.2.3


From 143c8e42e15ae1ed4b5a2353a64b3a4ba77bd337 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 25 Sep 2020 14:49:48 -0500
Subject: Changed edit_data_change and block_by_index to use DataTables API

* wqflask/wqflask/static/new/javascript/show_trait.js - Changed
edit_data_change to use DataTables API to fetch the list of names,
values, and (where applicable) standard errors in a way that just looks
at those columns (previously it iterated through all rows).
block_by_index was also changed to look just at columns
---
 .../wqflask/static/new/javascript/show_trait.js    | 66 ++++++++++------------
 1 file changed, 31 insertions(+), 35 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 40db07d7..a6f56d15 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -446,18 +446,25 @@ edit_data_change = function() {
     table = tables[_i];
     if ($('#' + table).length){
       table_api = $('#' + table).DataTable();
-      table_api.rows().eq(0).each( function ( index ) {
-        var row = primary_table.row( index );
-        sample_val = primary_table.cell(index, 3).nodes().to$().find('.edit_sample_value').val()
-        sample_name = $.trim(primary_table.cell(index, 2).nodes().to$().find('.edit_sample_sample_name').html())
+      sample_vals = [];
+      name_nodes = table_api.column(2).nodes().to$();
+      val_nodes = table_api.column(3).nodes().to$();
+      var_nodes = table_api.column(5).nodes().to$();
+      for (_j = 0; _j < val_nodes.length; _j++){
+        sample_val = val_nodes[_j].childNodes[0].value
+        sample_name = $.trim(name_nodes[_j].childNodes[0].textContent)
         if (is_number(sample_val) && sample_val !== "") {
           sample_val = parseFloat(sample_val);
           sample_sets[table].add_value(sample_val);
-          sample_var = primary_table.cell(index, 5).nodes().to$().find('.edit_sample_se').val()
-          if (is_number(sample_var)) {
-            sample_var = parseFloat(sample_var)
-          } else {
+          if (typeof var_nodes !== 'undefined'){
             sample_var = null;
+          } else {
+            sample_var = var_nodes[_j].childNodes[0].value
+            if (is_number(sample_var)) {
+              sample_var = parseFloat(sample_var)
+            } else {
+              sample_var = null;
+            }
           }
           sample_dict = {
             value: sample_val,
@@ -470,7 +477,7 @@ edit_data_change = function() {
             already_seen[sample_name] = true;
           }
         }
-      } );
+      }
     }
   }
 
@@ -557,7 +564,9 @@ populate_sample_attributes_values_dropdown = function() {
   return _results;
 };
 
-populate_sample_attributes_values_dropdown();
+if (Object.keys(js_data.attributes).length){
+  populate_sample_attributes_values_dropdown();
+}
 
 $('#exclude_menu').change(populate_sample_attributes_values_dropdown);
 block_by_attribute_value = function() {
@@ -583,20 +592,6 @@ block_by_index = function() {
   _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 = 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) {
-        error = _error;
-        alert("Syntax error");
-      }
-    }
-    */
     if (index_set.indexOf('-') !== -1) {
       try {
         start_index = parseInt(index_set.split("-")[0]);
@@ -614,19 +609,18 @@ block_by_index = function() {
     }
   }
   _results = [];
+  let block_group = $('#block_group').val();
+  if (block_group === "other") {
+    table_api = $('#samples_other').DataTable();
+  } else {
+    table_api = $('#samples_primary').DataTable();
+  }
+  val_nodes = table_api.column(3).nodes().to$();
   for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) {
     index = index_list[_k];
-    if ($('#block_group').val() === "primary") {
-      _results.push($('#samples_primary').find('td.column_name-Index').filter(function() { return $(this).text() == index.toString()  }).closest('tr').find('.trait_value_input').val("x"));
-    } else if ($('#block_group').val() === "other") {
-      _results.push($('#samples_other').find('td.column_name-Index').filter(function() { return $(this).text() == index.toString()  }).closest('tr').find('.trait_value_input').val("x"));
-    } else {
-      _results.push(void 0);
-    }
+    val_nodes[index - 1].childNodes[0].value = "x";
   }
-  return _results;
 };
-$('#block_by_index').click(block_by_index);
 
 hide_no_value = function() {
   return $('.value_se').each((function(_this) {
@@ -1450,8 +1444,10 @@ $('.stats_panel').click(function() {
   }
 });
 
-$('.edit_sample_value').change(edit_data_change);
-$('#block_by_index').click(edit_data_change);
+$('#block_by_index').click(function(){
+  block_by_index();
+  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 37500c0c36fbbb2b4ab291cf164b5397776357a7 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 25 Sep 2020 14:52:40 -0500
Subject: Fixed issue where attribute columns' alignment was offset by 1

* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
- attribute cells' alignment and column names were wrong because they were referring to an attribute offset by 1 in the attribute list
-
---
 .../wqflask/static/new/javascript/initialize_show_trait_tables.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
index 53d5b3f7..71eae87f 100644
--- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
+++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -147,8 +147,8 @@ var primary_table = $('#samples_primary').DataTable( {
 
       sorted_key_list = Object.keys(js_data.attributes).sort()
       for (i=0; i < sorted_key_list.length; i++) {
-        $('td', row).eq(attribute_start_pos + i).addClass("column_name-" + js_data.attributes[sorted_key_list[i]].name)
-        $('td', row).eq(attribute_start_pos + i).attr("style", "text-align: " + js_data.attributes[sorted_key_list[i]].alignment + "; padding-top: 2px; padding-bottom: 0px;")
+        $('td', row).eq(attribute_start_pos + i + 1).addClass("column_name-" + js_data.attributes[sorted_key_list[i]].name)
+        $('td', row).eq(attribute_start_pos + i + 1).attr("style", "text-align: " + js_data.attributes[sorted_key_list[i]].alignment + "; padding-top: 2px; padding-bottom: 0px;")
       }
     },
     'data': js_data['sample_lists'][0],
@@ -205,8 +205,8 @@ if (js_data.sample_lists.length > 1){
 
         sorted_key_list = Object.keys(js_data.attributes).sort()
         for (i=0; i < sorted_key_list.length; i++) {
-          $('td', row).eq(attribute_start_pos + i).addClass("column_name-" + js_data.attributes[sorted_key_list[i]].name)
-          $('td', row).eq(attribute_start_pos + i).attr("style", "text-align: " + js_data.attributes[sorted_key_list[i]].alignment + "; padding-top: 2px; padding-bottom: 0px;")
+          $('td', row).eq(attribute_start_pos + i + 1).addClass("column_name-" + js_data.attributes[sorted_key_list[i]].name)
+          $('td', row).eq(attribute_start_pos + i + 1).attr("style", "text-align: " + js_data.attributes[sorted_key_list[i]].alignment + "; padding-top: 2px; padding-bottom: 0px;")
         }
       },
       'data': js_data['sample_lists'][1],
-- 
cgit v1.2.3


From a1d6d81ceddd757370cd093aae6feeafa30d3858 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 2 Oct 2020 15:23:14 -0500
Subject: There were two copies of the "submit_special" function in both
 show_trait.js and show_trait_mapping_tools.js. The latter now just calls the
 function from the former

* wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js - Everything in this file was previously inside its own function, which made its functions unable to access the functions from show_trait.js (and necessitated it having its own "copy" of the submit_special function
---
 .../new/javascript/show_trait_mapping_tools.js     | 545 ++++++++++-----------
 1 file changed, 268 insertions(+), 277 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 4dce0705..c0f36eaa 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -1,307 +1,298 @@
-// Generated by CoffeeScript 1.8.0
-(function() {
-  var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, outlier_text, showalert, submit_special, toggle_enable_disable, update_time_remaining;
+var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, outlier_text, showalert, submit_special, toggle_enable_disable, update_time_remaining;
 
-  submit_special = function(url) {
-    $("#trait_data_form").attr("action", url);
-    $("#trait_data_form").submit();
-  };
-
-  update_time_remaining = function(percent_complete) {
-    var minutes_remaining, now, period, total_seconds_remaining;
-    now = new Date();
-    period = now.getTime() - root.start_time;
-    console.log("period is:", period);
-    if (period > 8000) {
-      total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000;
-      minutes_remaining = Math.round(total_seconds_remaining / 60);
-      if (minutes_remaining < 3) {
-        return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining");
-      } else {
-        return $('#time_remaining').text(minutes_remaining + " minutes remaining");
-      }
+update_time_remaining = function(percent_complete) {
+  var minutes_remaining, now, period, total_seconds_remaining;
+  now = new Date();
+  period = now.getTime() - root.start_time;
+  console.log("period is:", period);
+  if (period > 8000) {
+    total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000;
+    minutes_remaining = Math.round(total_seconds_remaining / 60);
+    if (minutes_remaining < 3) {
+      return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining");
+    } else {
+      return $('#time_remaining').text(minutes_remaining + " minutes remaining");
     }
-  };
+  }
+};
 
-  get_progress = function() {
-    var params, params_str, temp_uuid, url;
-    console.log("temp_uuid:", $("#temp_uuid").val());
-    temp_uuid = $("#temp_uuid").val();
-    params = {
-      key: temp_uuid
-    };
-    params_str = $.param(params);
-    url = "/get_temp_data?" + params_str;
-    console.log("url:", url);
-    $.ajax({
-      type: "GET",
-      url: url,
-      success: (function(_this) {
-        return function(progress_data) {
-          var percent_complete;
-          percent_complete = progress_data['percent_complete'];
-          console.log("in get_progress data:", progress_data);
-          $('#marker_regression_progress').css("width", percent_complete + "%");
-          if (root.start_time) {
-            if (!isNaN(percent_complete)) {
-              return update_time_remaining(percent_complete);
-            }
-          } else {
-            return root.start_time = new Date().getTime();
-          }
-        };
-      })(this)
-    });
-    return false;
+get_progress = function() {
+  var params, params_str, temp_uuid, url;
+  console.log("temp_uuid:", $("#temp_uuid").val());
+  temp_uuid = $("#temp_uuid").val();
+  params = {
+    key: temp_uuid
   };
-
-  block_outliers = function() {
-    return $('.outlier').each((function(_this) {
-      return function(_index, element) {
-        return $(element).find('.trait_value_input').val('x');
+  params_str = $.param(params);
+  url = "/get_temp_data?" + params_str;
+  console.log("url:", url);
+  $.ajax({
+    type: "GET",
+    url: url,
+    success: (function(_this) {
+      return function(progress_data) {
+        var percent_complete;
+        percent_complete = progress_data['percent_complete'];
+        console.log("in get_progress data:", progress_data);
+        $('#marker_regression_progress').css("width", percent_complete + "%");
+        if (root.start_time) {
+          if (!isNaN(percent_complete)) {
+            return update_time_remaining(percent_complete);
+          }
+        } else {
+          return root.start_time = new Date().getTime();
+        }
       };
-    })(this));
-  };
-
-  do_ajax_post = function(url, form_data) {
-    $.ajax({
-      type: "POST",
-      url: url,
-      data: form_data,
-      error: (function(_this) {
-        return function(xhr, ajaxOptions, thrownError) {
-          alert("Sorry, an error occurred");
-          console.log(xhr);
-          clearInterval(_this.my_timer);
-          $('#progress_bar_container').modal('hide');
-          $('#static_progress_bar_container').modal('hide');
-          return $("body").html("We got an error.");
-        };
-      })(this),
-      success: (function(_this) {
-        return function(data) {
-          clearInterval(_this.my_timer);
-          $('#progress_bar_container').modal('hide');
-          $('#static_progress_bar_container').modal('hide');
-          return open_mapping_results(data);
-        };
-      })(this)
-    });
-    console.log("settingInterval");
-    this.my_timer = setInterval(get_progress, 1000);
-    return false;
-  };
-
-  open_mapping_results = function(data) {
-    return $.colorbox({
-      html: data,
-      href: "#mapping_results_holder",
-      height: "90%",
-      width: "90%",
-      onComplete: (function(_this) {
-        return function() {
-          var filename, getSvgXml;
-          root.create_lod_chart();
-          filename = "lod_chart_" + js_data.this_trait;
-          getSvgXml = function() {
-            var svg;
-            svg = $("#topchart").find("svg")[0];
-            return (new XMLSerializer).serializeToString(svg);
-          };
-          $("#exportform > #export").click(function() {
-            var form, svg_xml;
-            svg_xml = getSvgXml();
-            form = $("#exportform");
-            form.find("#data").val(svg_xml);
-            form.find("#filename").val(filename);
-            return form.submit();
-          });
-          return $("#exportpdfform > #export_pdf").click(function() {
-            var form, svg_xml;
-            svg_xml = getSvgXml();
-            form = $("#exportpdfform");
-            form.find("#data").val(svg_xml);
-            form.find("#filename").val(filename);
-            return form.submit();
-          });
-        };
-      })(this)
-    });
-  };
-
-  outlier_text = "One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results.";
-  showalert = function(message, alerttype) {
-    return $('#outlier_alert_placeholder').append('<div id="mapping_alert" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
-  };
-
-  $('#suggestive').hide();
+    })(this)
+  });
+  return false;
+};
 
-  $('input[name=display_all]').change((function(_this) {
-    return function() {
-      console.log("check");
-      if ($('input[name=display_all]:checked').val() === "False") {
-        return $('#suggestive').show();
-      } else {
-        return $('#suggestive').hide();
-      }
+block_outliers = function() {
+  return $('.outlier').each((function(_this) {
+    return function(_index, element) {
+      return $(element).find('.trait_value_input').val('x');
     };
   })(this));
+};
 
-  //ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping
-  var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
-                            'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
-                            'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', 
-                            'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 
-                            'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples']
-
-  $(".rqtl_tab, #rqtl_geno_compute").on("click", (function(_this) {
-    return function() {
-      if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_geno_compute"){
-        var form_data, url;
-        url = "/loading";
-        $('input[name=method]').val("rqtl_geno");
-        $('input[name=selected_chr]').val($('#chr_rqtl_geno').val());
-        $('input[name=mapping_scale]').val($('#scale_rqtl_geno').val());
-        $('input[name=genofile]').val($('#genofile_rqtl_geno').val());
-        $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
-        $('input[name=categorical_vars]').val(js_data.categorical_vars)
-        $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val());
-        $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val());
-        $('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').val());
-        $('input[name=tool_used]').val("Mapping");
-        $('input[name=form_url]').val("/run_mapping");
-        $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
-        return submit_special(url);
-      } else {
-        return true
-      }
-    };
-  })(this));
-  
-  $(".gemma_tab, #gemma_compute").on("click", (function(_this) {
-    return function() {
-      if ($(this).hasClass('active') || $(this).attr('id') == "gemma_compute"){
-        var form_data, url;
-        console.log("RUNNING GEMMA");
-        url = "/loading";
-        $('input[name=method]').val("gemma");
-        $('input[name=selected_chr]').val($('#chr_gemma').val());
-        $('input[name=num_perm]').val(0);
-        $('input[name=genofile]').val($('#genofile_gemma').val());
-        $('input[name=maf]').val($('input[name=maf_gemma]').val());
-        $('input[name=tool_used]').val("Mapping");
-        $('input[name=form_url]').val("/run_mapping");
-        $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
-        return submit_special(url);
-      } else {
-        return true
-      }
-    };
-  })(this));
+do_ajax_post = function(url, form_data) {
+  $.ajax({
+    type: "POST",
+    url: url,
+    data: form_data,
+    error: (function(_this) {
+      return function(xhr, ajaxOptions, thrownError) {
+        alert("Sorry, an error occurred");
+        console.log(xhr);
+        clearInterval(_this.my_timer);
+        $('#progress_bar_container').modal('hide');
+        $('#static_progress_bar_container').modal('hide');
+        return $("body").html("We got an error.");
+      };
+    })(this),
+    success: (function(_this) {
+      return function(data) {
+        clearInterval(_this.my_timer);
+        $('#progress_bar_container').modal('hide');
+        $('#static_progress_bar_container').modal('hide');
+        return open_mapping_results(data);
+      };
+    })(this)
+  });
+  console.log("settingInterval");
+  this.my_timer = setInterval(get_progress, 1000);
+  return false;
+};
 
-  $(".reaper_tab, #interval_mapping_compute").on("click", (function(_this) {
-    return function() {
-      if ($(this).hasClass('active') || $(this).attr('id') == "interval_mapping_compute"){
-        var form_data, url;
-        console.log("In interval mapping");
-        url = "/loading";
-        $('input[name=method]').val("reaper");
-        $('input[name=selected_chr]').val($('#chr_reaper').val());
-        $('input[name=mapping_scale]').val($('#scale_reaper').val());
-        $('input[name=genofile]').val($('#genofile_reaper').val());
-        $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val());
-        $('input[name=control_marker]').val($('input[name=control_reaper]').val());
-        $('input[name=do_control]').val($('input[name=do_control_reaper]:checked').val());
-        $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val());
-        $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'));
-        $('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
-        $('input[name=tool_used]').val("Mapping");
-        $('input[name=form_url]').val("/run_mapping");
-        $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
-        return submit_special(url);
-      } else {
-        return true
-      }
-    };
-  })(this));
+open_mapping_results = function(data) {
+  return $.colorbox({
+    html: data,
+    href: "#mapping_results_holder",
+    height: "90%",
+    width: "90%",
+    onComplete: (function(_this) {
+      return function() {
+        var filename, getSvgXml;
+        root.create_lod_chart();
+        filename = "lod_chart_" + js_data.this_trait;
+        getSvgXml = function() {
+          var svg;
+          svg = $("#topchart").find("svg")[0];
+          return (new XMLSerializer).serializeToString(svg);
+        };
+        $("#exportform > #export").click(function() {
+          var form, svg_xml;
+          svg_xml = getSvgXml();
+          form = $("#exportform");
+          form.find("#data").val(svg_xml);
+          form.find("#filename").val(filename);
+          return form.submit();
+        });
+        return $("#exportpdfform > #export_pdf").click(function() {
+          var form, svg_xml;
+          svg_xml = getSvgXml();
+          form = $("#exportpdfform");
+          form.find("#data").val(svg_xml);
+          form.find("#filename").val(filename);
+          return form.submit();
+        });
+      };
+    })(this)
+  });
+};
 
-  $("#interval_mapping_compute, #gemma_compute, rqtl_geno_compute").on("mouseover", (function(_this) {
-    return function() {
-      if ($(".outlier").length && $(".outlier-alert").length < 1) {
-        return showalert(outlier_text, "alert-success outlier-alert");
-      }
-    };
-  })(this));
+outlier_text = "One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results.";
+showalert = function(message, alerttype) {
+  return $('#outlier_alert_placeholder').append('<div id="mapping_alert" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
+};
 
-  composite_mapping_fields = function() {
-    return $(".composite_fields").toggle();
-  };
+$('#suggestive').hide();
 
-  mapping_method_fields = function() {
-    return $(".mapping_method_fields").toggle();
+$('input[name=display_all]').change((function(_this) {
+  return function() {
+    console.log("check");
+    if ($('input[name=display_all]:checked').val() === "False") {
+      return $('#suggestive').show();
+    } else {
+      return $('#suggestive').hide();
+    }
   };
+})(this));
 
-  $("#use_composite_choice").change(composite_mapping_fields);
-
-  $("#mapping_method_choice").change(mapping_method_fields);
+//ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping
+var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
+                          'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
+                          'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', 
+                          'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 
+                          'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples']
 
-  $("#mapmodel_rqtl_geno").change(function() {
-    if ($(this).val() == "np"){
-      $("#mapmethod_rqtl_geno").attr('disabled', 'disabled');
-      $("#mapmethod_rqtl_geno").css('background-color', '#CCC');
-      $("#missing_geno").attr('disabled', 'disabled');
-      $("#missing_geno").css('background-color', '#CCC');
+$(".rqtl_tab, #rqtl_geno_compute").on("click", (function(_this) {
+  return function() {
+    if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_geno_compute"){
+      var form_data, url;
+      url = "/loading";
+      $('input[name=method]').val("rqtl_geno");
+      $('input[name=selected_chr]').val($('#chr_rqtl_geno').val());
+      $('input[name=mapping_scale]').val($('#scale_rqtl_geno').val());
+      $('input[name=genofile]').val($('#genofile_rqtl_geno').val());
+      $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
+      $('input[name=categorical_vars]').val(js_data.categorical_vars)
+      $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val());
+      $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val());
+      $('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').val());
+      $('input[name=tool_used]').val("Mapping");
+      $('input[name=form_url]').val("/run_mapping");
+      $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
+      return submit_special(url);
     } else {
-      $("#mapmethod_rqtl_geno").removeAttr('disabled');
-      $("#mapmethod_rqtl_geno").css('background-color', '#FFF');
-      $("#missing_geno").removeAttr('disabled');
-      $("#missing_geno").css('background-color', '#FFF');
+      return true
     }
-  });
+  };
+})(this));
 
-  $("#mapmethod_rqtl_geno").change(function() {
-    if ($(this).val() == "mr"){
-      $("#missing_geno_div").css('display', 'block');
+$(".gemma_tab, #gemma_compute").on("click", (function(_this) {
+  return function() {
+    if ($(this).hasClass('active') || $(this).attr('id') == "gemma_compute"){
+      var form_data, url;
+      console.log("RUNNING GEMMA");
+      url = "/loading";
+      $('input[name=method]').val("gemma");
+      $('input[name=selected_chr]').val($('#chr_gemma').val());
+      $('input[name=num_perm]').val(0);
+      $('input[name=genofile]').val($('#genofile_gemma').val());
+      $('input[name=maf]').val($('input[name=maf_gemma]').val());
+      $('input[name=tool_used]').val("Mapping");
+      $('input[name=form_url]').val("/run_mapping");
+      $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
+      return submit_special(url);
     } else {
-      $("#missing_geno_div").css('display', 'none');
+      return true
     }
-  });
+  };
+})(this));
 
-  $("li.mapping_tab").click(function() {
-    if ($(this).hasClass("rqtl")){
-      $(".rqtl_description").css("display", "block");
+$(".reaper_tab, #interval_mapping_compute").on("click", (function(_this) {
+  return function() {
+    if ($(this).hasClass('active') || $(this).attr('id') == "interval_mapping_compute"){
+      var form_data, url;
+      console.log("In interval mapping");
+      url = "/loading";
+      $('input[name=method]').val("reaper");
+      $('input[name=selected_chr]').val($('#chr_reaper').val());
+      $('input[name=mapping_scale]').val($('#scale_reaper').val());
+      $('input[name=genofile]').val($('#genofile_reaper').val());
+      $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val());
+      $('input[name=control_marker]').val($('input[name=control_reaper]').val());
+      $('input[name=do_control]').val($('input[name=do_control_reaper]:checked').val());
+      $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val());
+      $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'));
+      $('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
+      $('input[name=tool_used]').val("Mapping");
+      $('input[name=form_url]').val("/run_mapping");
+      $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
+      return submit_special(url);
     } else {
-      $(".rqtl_description").css("display", "none");
+      return true
     }
-  });
+  };
+})(this));
 
-  toggle_enable_disable = function(elem) {
-    return $(elem).prop("disabled", !$(elem).prop("disabled"));
+$("#interval_mapping_compute, #gemma_compute, rqtl_geno_compute").on("mouseover", (function(_this) {
+  return function() {
+    if ($(".outlier").length && $(".outlier-alert").length < 1) {
+      return showalert(outlier_text, "alert-success outlier-alert");
+    }
   };
+})(this));
 
-  $("#choose_closet_control").change(function() {
-    return toggle_enable_disable("#control_locus");
-  });
+composite_mapping_fields = function() {
+  return $(".composite_fields").toggle();
+};
 
-  $("#display_all_lrs").change(function() {
-    return toggle_enable_disable("#suggestive_lrs");
-  });
+mapping_method_fields = function() {
+  return $(".mapping_method_fields").toggle();
+};
 
-  $('#genofile_rqtl_geno').change(function() {
-    geno_location = $(this).children("option:selected").val().split(":")[0]
-    $('#scale_rqtl_geno').empty()
-    the_scales = js_data.scales_in_geno[geno_location]
-    for (var i = 0; i < the_scales.length; i++){
-      $('#scale_rqtl_geno').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1]));
-    }
-  });
-  $('#genofile_reaper').change(function() {
-    geno_location = $(this).children("option:selected").val().split(":")[0]
-    $('#scale_reaper').empty()
-    the_scales = js_data.scales_in_geno[geno_location]
-    for (var i = 0; i < the_scales.length; i++){
-      $('#scale_reaper').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1]));
-    }
-  });
+$("#use_composite_choice").change(composite_mapping_fields);
+
+$("#mapping_method_choice").change(mapping_method_fields);
+
+$("#mapmodel_rqtl_geno").change(function() {
+  if ($(this).val() == "np"){
+    $("#mapmethod_rqtl_geno").attr('disabled', 'disabled');
+    $("#mapmethod_rqtl_geno").css('background-color', '#CCC');
+    $("#missing_geno").attr('disabled', 'disabled');
+    $("#missing_geno").css('background-color', '#CCC');
+  } else {
+    $("#mapmethod_rqtl_geno").removeAttr('disabled');
+    $("#mapmethod_rqtl_geno").css('background-color', '#FFF');
+    $("#missing_geno").removeAttr('disabled');
+    $("#missing_geno").css('background-color', '#FFF');
+  }
+});
+
+$("#mapmethod_rqtl_geno").change(function() {
+  if ($(this).val() == "mr"){
+    $("#missing_geno_div").css('display', 'block');
+  } else {
+    $("#missing_geno_div").css('display', 'none');
+  }
+});
+
+$("li.mapping_tab").click(function() {
+  if ($(this).hasClass("rqtl")){
+    $(".rqtl_description").css("display", "block");
+  } else {
+    $(".rqtl_description").css("display", "none");
+  }
+});
+
+toggle_enable_disable = function(elem) {
+  return $(elem).prop("disabled", !$(elem).prop("disabled"));
+};
+
+$("#choose_closet_control").change(function() {
+  return toggle_enable_disable("#control_locus");
+});
+
+$("#display_all_lrs").change(function() {
+  return toggle_enable_disable("#suggestive_lrs");
+});
 
-}).call(this);
+$('#genofile_rqtl_geno').change(function() {
+  geno_location = $(this).children("option:selected").val().split(":")[0]
+  $('#scale_rqtl_geno').empty()
+  the_scales = js_data.scales_in_geno[geno_location]
+  for (var i = 0; i < the_scales.length; i++){
+    $('#scale_rqtl_geno').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1]));
+  }
+});
+$('#genofile_reaper').change(function() {
+  geno_location = $(this).children("option:selected").val().split(":")[0]
+  $('#scale_reaper').empty()
+  the_scales = js_data.scales_in_geno[geno_location]
+  for (var i = 0; i < the_scales.length; i++){
+    $('#scale_reaper').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1]));
+  }
+});
-- 
cgit v1.2.3


From 23b6c0a2329c589db2b121584abaa06abe0d60da Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 2 Oct 2020 15:42:17 -0500
Subject: Added function that pulls input data out of table and inserts it as
 hidden input elements in the form (so form submission can work with Scroller)

* wqflask/wqflask/static/new/javascript/show_trait.js - Added function "get_table_contents_for_form_submit" that is called with submit_special (that is called for correlations and mapping from the trait page)
---
 .../wqflask/static/new/javascript/show_trait.js    | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index a6f56d15..cde92160 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -499,6 +499,7 @@ edit_data_change = function() {
     return update_prob_plot();
   }
 };
+
 show_hide_outliers = function() {
   var label;
   label = $('#show_hide_outliers').val();
@@ -509,6 +510,7 @@ show_hide_outliers = function() {
     return console.log("Should be now Hide Outliers");
   }
 };
+
 on_corr_method_change = function() {
   var corr_method;
   corr_method = $('select[name=corr_type]').val();
@@ -523,10 +525,30 @@ on_corr_method_change = function() {
 $('select[name=corr_type]').change(on_corr_method_change);
 
 submit_special = function(url) {
+  get_table_contents_for_form_submit("trait_data_form");
   $("#trait_data_form").attr("action", url);
   $("#trait_data_form").submit();
 };
 
+get_table_contents_for_form_submit = function(form_id) {
+  // Borrowed code from - https://stackoverflow.com/questions/31418047/how-to-post-data-for-the-whole-table-using-jquery-datatables
+  let this_form = $("#" + form_id);
+  var params = primary_table.$('input').serializeArray();
+
+  $.each(params, function(){
+    // If element doesn't exist in DOM
+    if(!$.contains(document, this_form[this.name])){
+       // Create a hidden element
+       this_form.append(
+          $('<input>')
+             .attr('type', 'hidden')
+             .attr('name', this.name)
+             .val(this.value)
+       );
+    }
+ });
+}
+
 var corr_input_list = ['corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
                         'corr_return_results', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
 
-- 
cgit v1.2.3


From a3d9dad939a12d7c24fb9a125b973b7533db3824 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 2 Oct 2020 16:45:57 -0500
Subject: Converted transform functions to use DataTables API to work with
 scroller + fixed them to take into account blocked samples

* wqflask/wqflask/static/new/javascript/show_trait.js - Changed transform/normalize functions to use DataTables API to fetch and change values and also changed the way that code is structured to avoid a lot of duplicated code
---
 .../wqflask/static/new/javascript/show_trait.js    | 156 ++++++++++-----------
 1 file changed, 75 insertions(+), 81 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index cde92160..8b9a57a3 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -654,6 +654,7 @@ hide_no_value = function() {
   })(this));
 };
 $('#hide_no_value').click(hide_no_value);
+
 block_outliers = function() {
   return $('.outlier').each((function(_this) {
     return function(_index, element) {
@@ -662,6 +663,7 @@ block_outliers = function() {
   })(this));
 };
 $('#block_outliers').click(block_outliers);
+
 reset_samples_table = function() {
   $('input[name="transform"]').val("");
   $('span[name="transform_text"]').text("")
@@ -677,96 +679,56 @@ $('.reset').click(function() {
   edit_data_change();
 });
 
-log2_normalize_data = function(zero_to_one_vals_exist) {
-  return $('.trait_value_input').each((function(_this) {
-    return function(_index, element) {
-      current_value = $(element).data("value")
-      if(isNaN(current_value)) {
-        return current_value
-      } else {
-        if (zero_to_one_vals_exist){
-          current_value = parseFloat(current_value) + 1;
-        }
-        $(element).val(Math.log2(current_value).toFixed(3));
-        return Math.log2(current_value).toFixed(3)
-      }
-    };
-  })(this));
+log2_data = function(this_node) {
+  current_value = this_node.value;
+  if(!isNaN(current_value)) {
+    if (zero_to_one_vals_exist){
+      current_value = parseFloat(current_value) + 1;
+    }
+    this_node.value = Math.log2(current_value).toFixed(3);
+  }
 };
 
-log10_normalize_data = function(zero_to_one_vals_exist) {
-  return $('.trait_value_input').each((function(_this) {
-    return function(_index, element) {
-      current_value = $(element).data("value")
-      if(isNaN(current_value)) {
-        return current_value
-      } else {
-        if (zero_to_one_vals_exist){
-          current_value = parseFloat(current_value) + 1;
-        }
-        $(element).val(Math.log10(current_value).toFixed(3));
-        return Math.log10(current_value).toFixed(3)
-      }
-    };
-  })(this));
+log10_data = function() {
+  current_value = this_node.value;
+  if(!isNaN(current_value)) {
+    if (zero_to_one_vals_exist){
+      current_value = parseFloat(current_value) + 1;
+    }
+    this_node.value = Math.log10(current_value).toFixed(3);
+  }
 };
 
 
-sqrt_normalize_data = function() {
-  return $('.edit_sample_value').each((function(_this) {
-    return function(_index, element) {
-      current_value = parseFloat($(element).data("value")) + 1;
-      if(isNaN(current_value)) {
-        return current_value
-      } else {
-        $(element).val(Math.sqrt(current_value).toFixed(3));
-        return Math.sqrt(current_value).toFixed(3)
-      }
-    };
-  })(this));
+sqrt_data = function() {
+  current_value = this_node.value;
+  if(!isNaN(current_value)) {
+    this_node.value = Math.sqrt(current_value).toFixed(3);
+  }
 };
 
 invert_data = function() {
-  return $('.edit_sample_value').each((function(_this) {
-    return function(_index, element) {
-      current_value = parseFloat($(element).val());
-      if(isNaN(current_value)) {
-        return current_value
-      } else {
-        $(element).val(-(current_value));
-        return -(current_value)
-      }
-    };
-  })(this));
+  current_value = this_node.value;
+  if(!isNaN(current_value)) {
+    this_node.value = -(current_value);
+  }
 };
 
 
 qnorm_data = function() {
-  return $('.edit_sample_value').each((function(_this) {
-    return function(_index, element) {
-      current_value = parseFloat($(element).data("value")) + 1;
-      if(isNaN(current_value)) {
-        return current_value
-      } else {
-        $(element).val($(element).data("qnorm"));
-        return $(element).data("qnorm");
-      }
-    };
-  })(this));
+  current_value = this_node.value;
+  qnorm_value = this_node.attributes['data-qnorm'].value;
+  if(!isNaN(current_value)) {
+    this_node.value = qnorm_value;
+  }
 };
 
 zscore_data = function() {
-  return $('.edit_sample_value').each((function(_this) {
-    return function(_index, element) {
-      current_value = parseFloat($(element).data("value")) + 1;
-      if(isNaN(current_value)) {
-        return current_value
-      } else {
-        $(element).val($(element).data("zscore"));
-        return $(element).data("zscore");
-      }
-    };
-  })(this));
+  current_value = this_node.value;
+  qnorm_value = this_node.attributes['data-zscore'].value;
+  if(!isNaN(current_value)) {
+    this_node.value = qnorm_value;
+  }
 };
 
 check_for_zero_to_one_vals = function() {
@@ -786,15 +748,47 @@ check_for_zero_to_one_vals = function() {
   return zero_to_one_vals_exist
 }
 
+do_transform = function(transform_type) {
+  tables = ['samples_primary', 'samples_other'];
+  for (_i = 0, _len = tables.length; _i < _len; _i++) {
+    table = tables[_i];
+    if ($('#' + table).length) {
+      table_api = $('#' + table).DataTable();
+      val_nodes = table_api.column(3).nodes().to$();
+      for (i = 0; i < val_nodes.length; i++) {
+        this_node = val_nodes[i].childNodes[0]
+        if (transform_type == "log2"){
+          log2_data(this_node)
+        }
+        if (transform_type == "log10"){
+          log10_data(this_node)
+        }
+        if (transform_type == "sqrt"){
+          sqrt_data(this_node)
+        }
+        if (transform_type == "invert"){
+          invert_data(this_node)
+        }
+        if (transform_type == "qnorm"){
+          qnorm_data(this_node)
+        }
+        if (transform_type == "zscore"){
+          zscore_data(this_node)
+        }
+      }
+    }
+  }
+}
+
 normalize_data = function() {
   if ($('#norm_method option:selected').val() == 'log2' || $('#norm_method option:selected').val() == 'log10'){
     if ($('input[name="transform"]').val() != "log2" && $('#norm_method option:selected').val() == 'log2') {
-      log2_normalize_data(zero_to_one_vals_exist)
+      do_transform("log2")
       $('input[name="transform"]').val("log2")
       $('span[name="transform_text"]').text(" - log2 transformed")
     } else {
       if ($('input[name="transform"]').val() != "log10" && $('#norm_method option:selected').val() == 'log10'){
-        log10_normalize_data(zero_to_one_vals_exist)
+        do_transform("log10")
         $('input[name="transform"]').val("log10")
         $('span[name="transform_text"]').text(" - log10 transformed")
       }
@@ -802,26 +796,26 @@ normalize_data = function() {
   }
   else if ($('#norm_method option:selected').val() == 'sqrt'){
     if ($('input[name="transform"]').val() != "sqrt") {
-      sqrt_normalize_data()
+      do_transform("sqrt")
       $('input[name="transform"]').val("sqrt")
       $('span[name="transform_text"]').text(" - Square Root transformed")
     }
   }
   else if ($('#norm_method option:selected').val() == 'invert'){
-    invert_data()
+    do_transform("invert")
     $('input[name="transform"]').val("inverted")
     $('span[name="transform_text"]').text(" - Inverted")
   }
   else if ($('#norm_method option:selected').val() == 'qnorm'){
     if ($('input[name="transform"]').val() != "qnorm") {
-      qnorm_data()
+      do_transform("qnorm")
       $('input[name="transform"]').val("qnorm")
       $('span[name="transform_text"]').text(" - Quantile Normalized")
     }
   }
   else if ($('#norm_method option:selected').val() == 'zscore'){
     if ($('input[name="transform"]').val() != "zscore") {
-      zscore_data()
+      do_transform("zscore")
       $('input[name="transform"]').val("zscore")
       $('span[name="transform_text"]').text(" - Z-Scores")
     }
-- 
cgit v1.2.3


From f4cec3d4ae1083159521664d343c08340f59cfa8 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 5 Oct 2020 15:12:52 -0500
Subject: Fixed issue that was causing SE column to not show up in the trait
 page table

* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - Apparently "true" in js_data was a boolean instead of a string, so the previous if statements weren't working properly
---
 .../static/new/javascript/initialize_show_trait_tables.js      | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
index 71eae87f..ebed36d1 100644
--- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
+++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -2,10 +2,10 @@
 
 // ZS: This variable is just created to get the column position of the first case attribute (if case attributes exist), since it's needed to set the row classes in createdRow for the DataTable
 var attribute_start_pos = 3;
-if (js_data.se_exists === "true") {
+if (js_data.se_exists === true) {
   attribute_start_pos += 2;
 }
-if (js_data.has_num_cases === "true") {
+if (js_data.has_num_cases === true) {
   attribute_start_post += 1;
 }
 
@@ -48,7 +48,7 @@ build_columns = function() {
     }
   ];
 
-  if (js_data.se_exists === "true") {
+  if (js_data.se_exists === true) {
     column_list.push(
       {
         'bSortable': false,
@@ -130,7 +130,7 @@ var primary_table = $('#samples_primary').DataTable( {
       $('td', row).eq(1).addClass("column_name-Index")
       $('td', row).eq(2).addClass("column_name-Sample")
       $('td', row).eq(3).addClass("column_name-Value")
-      if (js_data.se_exists === "true") {
+      if (js_data.se_exists === true) {
         $('td', row).eq(5).addClass("column_name-SE")
         if (js_data.has_num_cases === "true") {
           $('td', row).eq(6).addClass("column_name-num_cases")
@@ -188,7 +188,7 @@ if (js_data.sample_lists.length > 1){
         $('td', row).eq(1).addClass("column_name-Index")
         $('td', row).eq(2).addClass("column_name-Sample")
         $('td', row).eq(3).addClass("column_name-Value")
-        if (js_data.se_exists === "true") {
+        if (js_data.se_exists === true) {
           $('td', row).eq(5).addClass("column_name-SE")
           if (js_data.has_num_cases === "true") {
             $('td', row).eq(6).addClass("column_name-num_cases")
-- 
cgit v1.2.3


From ebb515b9091237f5f3217517b3675675cbf56eb4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 5 Oct 2020 16:14:03 -0500
Subject: Added square root to the transform functions that are only active if
 there are no negative values

* wqflask/wqflask/templates/show_trait_transform_and_filter.html - made sqrt option contingent on no negative values
---
 .../templates/show_trait_transform_and_filter.html | 145 ++++++++++-----------
 1 file changed, 70 insertions(+), 75 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index b4118b04..9fb560a0 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -1,83 +1,78 @@
 <div>
-    <div class="form-horizontal">
-            <p>Edit or delete values in the Trait Data boxes, and use the
-                <strong>Reset</strong> option as
-                needed.
-            </p>
+  <div class="form-horizontal">
+          <p>Edit or delete values in the Trait Data boxes, and use the
+              <strong>Reset</strong> option as
+              needed.
+          </p>
 
-            <div id="blockMenuSpan" class="input-append" style="margin-bottom: 10px;">
-                <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">
-                  <option value="primary">
-                    {{ sample_group_types['samples_primary'] }}
-                  </option>
-                  <option value="other">
-                    {{ sample_group_types['samples_other'] }}
-                  </option>
-                </select>
-                <input type="button" id="block_by_index" class="btn btn-danger" value="Block">
-            </div>
-            <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" style="margin-top:10px; margin-bottom:10px;">
-                <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">
-              <input type="button" class="btn btn-success reset" value="Reset">
-              <span class="input-append">
-                <input type="button" class="btn btn-default export" value="Export">
-                <select class="select optional span2 export_format">
-                  <option value="excel">Excel</option>
-                  <option value="csv">CSV</option>
-                </select>
-              </span>
-              <br>
-              <div style="margin-top:10px;">
-              <input type="button" id="normalize" class="btn btn-success" value="Normalize">
-              <select id="norm_method" class="select optional span2">
-                {% if negative_vals_exist == "false" %}
-                <option value="log2">Log2</option>
-                <option value="log10">Log10</option>
-                {% endif %}
-                <option value="zscore">Z-score</option>
-                <option value="qnorm">Quantile</option>
-                <option value="sqrt">Square Root</option>
-                <option value="invert">Invert +/-</option>
+          <div id="blockMenuSpan" class="input-append" style="margin-bottom: 10px;">
+              <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">
+                <option value="primary">
+                  {{ sample_group_types['samples_primary'] }}
+                </option>
+                <option value="other">
+                  {{ sample_group_types['samples_other'] }}
+                </option>
+              </select>
+              <input type="button" id="block_by_index" class="btn btn-danger" value="Block">
+          </div>
+          <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" style="margin-top:10px; margin-bottom:10px;">
+              <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">
+            <input type="button" class="btn btn-success reset" value="Reset">
+            <span class="input-append">
+              <input type="button" class="btn btn-default export" value="Export">
+              <select class="select optional span2 export_format">
+                <option value="excel">Excel</option>
+                <option value="csv">CSV</option>
               </select>
-              </div>
-              <!--
-              {% if sample_groups[0].sample_qnorm is not none %}
-              <input type="button" id="qnorm" class="btn btn-default" value="Quantile Normalize">
+            </span>
+            <br>
+            <div style="margin-top:10px;">
+            <input type="button" id="normalize" class="btn btn-success" value="Normalize">
+            <select id="norm_method" class="select optional span2">
+              {% if negative_vals_exist == "false" %}
+              <option value="log2">Log2</option>
+              <option value="log10">Log10</option>
+              <option value="sqrt">Square Root</option>
               {% endif %}
-              -->
+              <option value="zscore">Z-score</option>
+              <option value="qnorm">Quantile</option>
+              <option value="invert">Invert +/-</option>
+            </select>
             </div>
-        <br>
+          </div>
+      <br>
 
-        <div>
-            <p>Outliers highlighted in
-                    <strong style="background-color:orange;">orange</strong>
-                    can be hidden using
-                    the <strong>Hide Outliers</strong> button.
-            </p>
+      <div>
+          <p>Outliers highlighted in
+                  <strong style="background-color:orange;">orange</strong>
+                  can be hidden using
+                  the <strong>Hide Outliers</strong> button.
+          </p>
 
-            <p>Samples with no value (x) can be hidden by clicking
-                    <strong>Hide No Value</strong> button.
-            </p>
-        </div>
-    </div>
+          <p>Samples with no value (x) can be hidden by clicking
+                  <strong>Hide No Value</strong> button.
+          </p>
+      </div>
+  </div>
 </div>
\ No newline at end of file
-- 
cgit v1.2.3


From 6b0a1c6359e0caeb8ae9f311f89d46dd8f837984 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 5 Oct 2020 16:14:57 -0500
Subject: Changed order of JS imports to both make DataTables objects available
 to all other JS code and move all local JS code below third-party libraries

* wqflask/wqflask/templates/show_trait.html - Changed order of JS imports
---
 wqflask/wqflask/templates/show_trait.html | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 0a79ad48..2d65f008 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -143,17 +143,18 @@
     <script type="text/javascript" src="/static/new/javascript/plotly_probability_plot.js"></script>
     <script type="text/javascript" src="/static/new/javascript/compare_traits_scatterplot.js"></script>
 
-    <script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script>
-    <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
-    <script type="text/javascript" src="/static/new/javascript/validation.js"></script>
 
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
     <script type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.2/js/dataTables.scroller.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/noUiSlider/nouislider.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/get_covariates_from_collection.js"></script>
+
     <script type="text/javascript" src="/static/new/javascript/initialize_show_trait_tables.js"></script>
+    <script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script>
+    <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
+    <script type="text/javascript" src="/static/new/javascript/validation.js"></script>
+    <script type="text/javascript" src="/static/new/javascript/get_covariates_from_collection.js"></script>
 
     <script type="text/javascript" charset="utf-8">
 
-- 
cgit v1.2.3


From c92504a72e3b0c017677abfdfd0dacf105295579 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 5 Oct 2020 16:17:29 -0500
Subject: Simplified if statements

* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - simplified if statements to just say if(js_data.se_exists) instead of if(js_data.se_exists === true)
---
 .../wqflask/static/new/javascript/initialize_show_trait_tables.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
index ebed36d1..5be3c790 100644
--- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
+++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -2,7 +2,7 @@
 
 // ZS: This variable is just created to get the column position of the first case attribute (if case attributes exist), since it's needed to set the row classes in createdRow for the DataTable
 var attribute_start_pos = 3;
-if (js_data.se_exists === true) {
+if (js_data.se_exists) {
   attribute_start_pos += 2;
 }
 if (js_data.has_num_cases === true) {
@@ -48,7 +48,7 @@ build_columns = function() {
     }
   ];
 
-  if (js_data.se_exists === true) {
+  if (js_data.se_exists) {
     column_list.push(
       {
         'bSortable': false,
@@ -130,7 +130,7 @@ var primary_table = $('#samples_primary').DataTable( {
       $('td', row).eq(1).addClass("column_name-Index")
       $('td', row).eq(2).addClass("column_name-Sample")
       $('td', row).eq(3).addClass("column_name-Value")
-      if (js_data.se_exists === true) {
+      if (js_data.se_exists) {
         $('td', row).eq(5).addClass("column_name-SE")
         if (js_data.has_num_cases === "true") {
           $('td', row).eq(6).addClass("column_name-num_cases")
@@ -188,7 +188,7 @@ if (js_data.sample_lists.length > 1){
         $('td', row).eq(1).addClass("column_name-Index")
         $('td', row).eq(2).addClass("column_name-Sample")
         $('td', row).eq(3).addClass("column_name-Value")
-        if (js_data.se_exists === true) {
+        if (js_data.se_exists) {
           $('td', row).eq(5).addClass("column_name-SE")
           if (js_data.has_num_cases === "true") {
             $('td', row).eq(6).addClass("column_name-num_cases")
-- 
cgit v1.2.3


From 47985414433542adc7e19f7298d71a9cf2472382 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 5 Oct 2020 16:19:04 -0500
Subject: Changed the way tranform functions work

* wqflask/wqflask/static/new/javascript/show_trait.js
- Changed transform options to only apply to original values, with the exception of the "invert" transform and rows where the value was set to "x"
- Only run "check_if_zero_to_one_vals" once on page load instead of running it every time a transform is run
- Changed Transform text to reflect when there's a combination of Invert and some other transform
- Updated Reset function to use DataTables API
---
 .../wqflask/static/new/javascript/show_trait.js    | 103 +++++++++++++--------
 1 file changed, 64 insertions(+), 39 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 8b9a57a3..092c890f 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -667,54 +667,92 @@ $('#block_outliers').click(block_outliers);
 reset_samples_table = function() {
   $('input[name="transform"]').val("");
   $('span[name="transform_text"]').text("")
-  return $('.trait_value_input').each((function(_this) {
-    return function(_index, element) {
-      $(element).val($(element).data('value'));
-      return $(element).parents('.value_se').show();
-    };
-  })(this));
+
+  tables = ['samples_primary', 'samples_other'];
+  for (_i = 0, _len = tables.length; _i < _len; _i++) {
+    table = tables[_i];
+    if ($('#' + table).length) {
+      table_api = $('#' + table).DataTable();
+      val_nodes = table_api.column(3).nodes().to$();
+      for (i = 0; i < val_nodes.length; i++) {
+        this_node = val_nodes[i].childNodes[0];
+        this_node.value = this_node.attributes["data-value"].value;
+      }
+      if (js_data.se_exists){
+        se_nodes = table_api.column(5).nodes().to$();
+        for (i = 0; i < val_nodes.length; i++) {
+          this_node = val_nodes[i].childNodes[0];
+          this_node.value = this_node.attributes["data-value"].value;
+        }
+      }
+    }
+  }
 };
 $('.reset').click(function() {
   reset_samples_table();
   edit_data_change();
 });
 
+check_for_zero_to_one_vals = function() {
+  tables = ['samples_primary', 'samples_other'];
+  for (_i = 0, _len = tables.length; _i < _len; _i++) {
+    table = tables[_i];
+    if ($('#' + table).length) {
+      table_api = $('#' + table).DataTable();
+      val_nodes = table_api.column(3).nodes().to$();
+      for (i = 0; i < val_nodes.length; i++) {
+        this_node = val_nodes[i].childNodes[0];
+        if(!isNaN(this_node.value)) {
+          if (0 <= this_node.value && this_node.value < 1){
+            return true
+          }
+        }
+      }
+    }
+  }
+  return false
+}
+
 log2_data = function(this_node) {
   current_value = this_node.value;
-  if(!isNaN(current_value)) {
+  original_value = this_node.attributes['data-value'].value;
+  if(!isNaN(current_value) && !isNaN(original_value)) {
     if (zero_to_one_vals_exist){
-      current_value = parseFloat(current_value) + 1;
+      original_value = parseFloat(original_value) + 1;
     }
-    this_node.value = Math.log2(current_value).toFixed(3);
+    this_node.value = Math.log2(original_value).toFixed(3);
   }
 };
 
 log10_data = function() {
   current_value = this_node.value;
-  if(!isNaN(current_value)) {
+  original_value = this_node.attributes['data-value'].value;
+  if(!isNaN(current_value) && !isNaN(original_value)) {
     if (zero_to_one_vals_exist){
-      current_value = parseFloat(current_value) + 1;
+      original_value = parseFloat(original_value) + 1;
     }
-    this_node.value = Math.log10(current_value).toFixed(3);
+    this_node.value = Math.log10(original_value).toFixed(3);
   }
 };
 
-
 sqrt_data = function() {
   current_value = this_node.value;
-  if(!isNaN(current_value)) {
-    this_node.value = Math.sqrt(current_value).toFixed(3);
+  original_value = this_node.attributes['data-value'].value;
+  if(!isNaN(current_value) && !isNaN(original_value)) {
+    if (zero_to_one_vals_exist){
+      original_value = parseFloat(original_value) + 1;
+    }
+    this_node.value = Math.sqrt(original_value).toFixed(3);
   }
 };
 
 invert_data = function() {
   current_value = this_node.value;
   if(!isNaN(current_value)) {
-    this_node.value = -(current_value);
+    this_node.value = parseFloat(-(current_value)).toFixed(3);
   }
 };
 
-
 qnorm_data = function() {
   current_value = this_node.value;
   qnorm_value = this_node.attributes['data-qnorm'].value;
@@ -725,29 +763,12 @@ qnorm_data = function() {
 
 zscore_data = function() {
   current_value = this_node.value;
-  qnorm_value = this_node.attributes['data-zscore'].value;
+  zscore_value = this_node.attributes['data-zscore'].value;
   if(!isNaN(current_value)) {
-    this_node.value = qnorm_value;
+    this_node.value = zscore_value;
   }
 };
 
-check_for_zero_to_one_vals = function() {
-  zero_to_one_vals_exist = false
-  $('.trait_value_input').each(function() {
-    current_value = $(this).data("value")
-    if(isNaN(current_value)) {
-      return true;
-    } else {
-      current_value = parseFloat(current_value)
-      if (0 <= current_value && current_value < 1){
-        zero_to_one_vals_exist = true
-        return false
-      }
-    }
-  });
-  return zero_to_one_vals_exist
-}
-
 do_transform = function(transform_type) {
   tables = ['samples_primary', 'samples_other'];
   for (_i = 0, _len = tables.length; _i < _len; _i++) {
@@ -804,7 +825,12 @@ normalize_data = function() {
   else if ($('#norm_method option:selected').val() == 'invert'){
     do_transform("invert")
     $('input[name="transform"]').val("inverted")
-    $('span[name="transform_text"]').text(" - Inverted")
+    if ($('span[name="transform_text"]:eq(0)').text() != ""){
+      current_text = $('span[name="transform_text"]:eq(0)').text();
+      $('span[name="transform_text"]').text(current_text + " + Inverted");
+    } else {
+      $('span[name="transform_text"]').text(" - Inverted")
+    }
   }
   else if ($('#norm_method option:selected').val() == 'qnorm'){
     if ($('input[name="transform"]').val() != "qnorm") {
@@ -822,11 +848,10 @@ normalize_data = function() {
   }
 }
 
-zero_to_one_vals_exist = false
+zero_to_one_vals_exist = check_for_zero_to_one_vals();
 
 show_transform_warning = function() {
   transform_type = $('#norm_method option:selected').val()
-  zero_to_one_vals_exist = check_for_zero_to_one_vals();
   if (transform_type == "log2" || transform_type == "log10"){
     if (zero_to_one_vals_exist){
       $('#transform_alert').css("display", "block")
-- 
cgit v1.2.3


From c30fdd56dd067b8d15724a24414fb4def5283ebd Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 5 Oct 2020 16:24:41 -0500
Subject: Replaced "+" with "and" in transform text

* wqflask/wqflask/static/new/javascript/show_trait.js - Replaced "+" with "and" when Invert and another transform are combined and capitalized "Transform"
---
 wqflask/wqflask/static/new/javascript/show_trait.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 092c890f..eaad0a4c 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -806,12 +806,12 @@ normalize_data = function() {
     if ($('input[name="transform"]').val() != "log2" && $('#norm_method option:selected').val() == 'log2') {
       do_transform("log2")
       $('input[name="transform"]').val("log2")
-      $('span[name="transform_text"]').text(" - log2 transformed")
+      $('span[name="transform_text"]').text(" - log2 Transformed")
     } else {
       if ($('input[name="transform"]').val() != "log10" && $('#norm_method option:selected').val() == 'log10'){
         do_transform("log10")
         $('input[name="transform"]').val("log10")
-        $('span[name="transform_text"]').text(" - log10 transformed")
+        $('span[name="transform_text"]').text(" - log10 Transformed")
       }
     }
   }
@@ -819,7 +819,7 @@ normalize_data = function() {
     if ($('input[name="transform"]').val() != "sqrt") {
       do_transform("sqrt")
       $('input[name="transform"]').val("sqrt")
-      $('span[name="transform_text"]').text(" - Square Root transformed")
+      $('span[name="transform_text"]').text(" - Square Root Transformed")
     }
   }
   else if ($('#norm_method option:selected').val() == 'invert'){
@@ -827,7 +827,7 @@ normalize_data = function() {
     $('input[name="transform"]').val("inverted")
     if ($('span[name="transform_text"]:eq(0)').text() != ""){
       current_text = $('span[name="transform_text"]:eq(0)').text();
-      $('span[name="transform_text"]').text(current_text + " + Inverted");
+      $('span[name="transform_text"]').text(current_text + " and Inverted");
     } else {
       $('span[name="transform_text"]').text(" - Inverted")
     }
-- 
cgit v1.2.3


From cfb45c4e6980e9f37b12ac4f4c2016ac8a37efe2 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 8 Oct 2020 14:52:49 -0500
Subject: Changed the min-width of trait page main div in order to allow trait
 descriptions to shrink to a smaller width (but not too small)

* wqflask/wqflask/templates/show_trait.html - Changed width of main container div to 700px
---
 wqflask/wqflask/templates/show_trait.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 56df2049..ea881917 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -37,7 +37,7 @@
         <input type="hidden" name="covariates" value="">
         <input type="hidden" name="transform" value="">
 
-        <div class="container" style="min-width: 1450px;">
+        <div class="container" style="min-width: 700px;">
             <div class="panel-group" id="accordion">
                 <div class="panel panel-default">
                     <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseOne" aria-expanded="true">
-- 
cgit v1.2.3


From a79e099d6ce428459affd44afc8f795dd7561fae Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 8 Oct 2020 14:54:02 -0500
Subject: Adjusted some widths/classes to allow correlation description text to
 expand/shrink with screen size and make drop-downs a better width

* wqflask/wqflask/templates/show_trait_calculate_correlations.html - Adjusted widths of drop-down divs and removed the col-width class from the description div (the right side) so it can shrink wqwith screen size
---
 .../wqflask/templates/show_trait_calculate_correlations.html | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 1378b91b..9420c9c6 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -1,5 +1,5 @@
 <div>
-  <div class="col-xs-7">
+  <div class="col-xs-6" style="min-width: 800px;">
     <div style="padding: 20px" class="form-horizontal">
         
         <div class="form-group">
@@ -39,7 +39,7 @@
         
         <div class="form-group">
             <label for="corr_return_results" class="col-xs-2 control-label">Return</label>
-            <div class="col-xs-3 controls">
+            <div class="col-xs-4 controls">
                 <select name="corr_return_results" class="form-control">
                     {% for return_result in corr_tools.return_results_menu %}
                         <option value="{{ return_result }}" 
@@ -55,7 +55,7 @@
         
         <div class="form-group">
             <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label>
-            <div class="col-xs-3 controls">
+            <div class="col-xs-4 controls">
                 <select name="corr_samples_group" class="form-control">
                     {% for group, pretty_group in sample_group_types.items() %}
                         <option value="{{ group }}">{{ pretty_group }}</option>
@@ -66,7 +66,7 @@
             
         <div id="corr_sample_method" class="form-group">
             <label for="corr_sample_method" class="col-xs-2 control-label">Type</label>
-            <div class="col-xs-3 controls">
+            <div class="col-xs-4 controls">
                 <select name="corr_sample_method" class="form-control">
                     <option value="pearson">Pearson</option>
                     <option value="spearman">Spearman Rank</option>
@@ -77,7 +77,7 @@
         {% if dataset.type != "Publish" %}
         <div class="form-group">
             <label class="col-xs-2 control-label">Min Expr</label>
-            <div class="col-xs-3 controls">
+            <div class="col-xs-4 controls">
                 <input name="min_expr" value="" type="text" class="form-control" style="width: 70px;">
             </div>
         </div>
@@ -114,7 +114,7 @@
         </div>
     </div>
   </div>
-  <div class="col-xs-5">
+  <div>
     <span id="sample_r_desc" class="correlation_desc fs12">
         The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a>
         is computed
-- 
cgit v1.2.3


From 205f2277493fca1d7b8a0520438767296a9c20d4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 8 Oct 2020 14:55:54 -0500
Subject: Allowed mapping method description text to shrink with screen size

* wqflask/wqflask/templates/show_trait_mapping_tools.html - Removed the "col-xs-_" class to allow the div containing mapping description text to shrink with screen size
---
 wqflask/wqflask/templates/show_trait_mapping_tools.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 27040045..94388b2f 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -397,8 +397,8 @@
             </div>
         </div>
     </div>
-    <div class="col-xs-7">
-        <dl style="width: 500px;">
+    <div>
+        <dl>
              {% for mapping_method in dataset.group.mapping_names %}
              {% if mapping_method == "GEMMA" %}
              <dt style="padding-top: 20px;">GEMMA</dt>
-- 
cgit v1.2.3


From ef49f885d5f668e50b3b8849012d3fec99483e2b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 9 Oct 2020 13:39:29 -0500
Subject: Change some column and overall table widths for search result table
 and view collections table + changed "Max LRS" column header to "High P"

* wqflask/wqflask/templates/collections/view.html - changed column widths and "Max LRS" header to "High P"
* wqflask/wqflask/templates/search_result_page.html - changed column widths and "Max LRS" header to "High P"
---
 wqflask/wqflask/templates/collections/view.html   | 16 ++++++++--------
 wqflask/wqflask/templates/search_result_page.html | 12 +++++-------
 2 files changed, 13 insertions(+), 15 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index bc487a59..d1a97310 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -8,7 +8,7 @@
 {% block content %}
 <!-- Start of body -->
 
-    <div class="container" style="min-width: 2050px;">
+    <div class="container">
         <h1>
             <span id="collection_name">{{ uc.name }}</span>
             <input type="text" name="new_collection_name" style="font-size: 20px; display: none; width: 500px;" class="form-control" placeholder="{{ uc.name }}"> 
@@ -85,7 +85,7 @@
             <div style="margin-top: 10px; margin-bottom: 5px;">
                 <b>Show/Hide Columns:</b>
             </div>
-            <div>
+            <div style="min-width: 1500px;">
                 <table class="table-hover table-striped cell-border" id='trait_table' style="float: left;">
                     <thead>
                         <tr>
@@ -97,7 +97,7 @@
                             <th data-export="Description">Description</th>
                             <th data-export="Location">Location</th>
                             <th data-export="Mean">Mean</th>
-                            <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
+                            <th data-export="Max LRS">High P <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
                             <th data-export="Peak Location">Peak Location</th>
                             <th data-export="Add. Eff.">Effect Size <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
                         </tr>
@@ -195,11 +195,11 @@
                     { 'type': "natural-minus-na", "width": 120 },
                     { "type": "natural" },
                     { "type": "natural"  },
-                    { "type": "natural", "width": 130 },
-                    { "type": "natural", "width": 35 },
-                    { "type": "natural", "width": 35 },
-                    { "type": "natural", "width": 130 },
-                    { "type": "natural" }
+                    { "type": "natural", "width": 125 },
+                    { "type": "natural", "width": 60 },
+                    { "type": "natural", "width": 60 },
+                    { "type": "natural", "width": 125 },
+                    { "type": "natural", "width": 85 }
                 ],
                 "order": [[1, "asc" ]],
                 buttons: [
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index e2e1aa46..2318bfb8 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -140,7 +140,6 @@
             <b>Show/Hide Columns:</b>
           </div>
           {% endif %}
-          <!--<div id="table_container" style="min-width: {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}2000{% else %}380{% endif %}px;">-->
           <div id="table_container" {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}style="min-width: 1500px;"{% endif %}>
             <table class="table-hover table-striped cell-border" id='trait_table' style="float: left; width: {% if dataset.type == 'Geno' %}380px{% else %}100%{% endif %};">
                 <tbody>
@@ -290,7 +289,6 @@
                     {
                       'title': "Description",
                       'type': "natural",
-                      'width': "500px",
                       'data': null,
                       'render': function(data, type, row, meta) {
                         try {
@@ -303,7 +301,7 @@
                     {
                       'title': "Location",
                       'type': "natural-minus-na",
-                      'width': "120px",
+                      'width': "125px",
                       'data': "location"
                     },
                     {
@@ -314,23 +312,23 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
+                      'title': "High P<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "lrs_score",
-                      'width': "80px",
+                      'width': "60px",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
                       'title': "Peak Location",
                       'type': "natural-minus-na",
-                      'width': "120px",
+                      'width': "125px",
                       'data': "lrs_location"
                     },
                     {
                       'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "additive",
-                      'width': "120px",
+                      'width': "85px",
                       'orderSequence': [ "desc", "asc"]
                     }{% elif dataset.type == 'Publish' %},
                     {
-- 
cgit v1.2.3


From 5fdb3b83566516782542d04b92a5be97f41c2330 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 13 Oct 2020 15:25:54 -0500
Subject: Added right-alignment for trait_value_input text fields in sample
 table to CSS file instead of setting it as a style in
 initialize_show_trait_tables.js

---
 wqflask/wqflask/static/new/css/show_trait.css                |  8 ++++++++
 .../static/new/javascript/initialize_show_trait_tables.js    | 12 ++++++------
 2 files changed, 14 insertions(+), 6 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 338302af..853819ea 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -46,4 +46,12 @@ table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td {
 table.dataTable.cell-border tbody tr th:first-child,
 table.dataTable.cell-border tbody tr td:first-child {
   border-left: 1px solid #ccc;
+}
+
+.checkbox {
+  min-height: 20px;
+}
+
+.trait_value_input {
+  text-align: right;
 }
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
index 5be3c790..97b71306 100644
--- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
+++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -16,7 +16,7 @@ build_columns = function() {
       'orderDataType': "dom-checkbox",
       'searchable' : false,
       'render': function(data, type, row, meta) {
-      return '<input type="checkbox" name="searchResult" style="min-height: 20px;" class="checkbox edit_sample_checkbox" value="">'
+      return '<input type="checkbox" name="searchResult" class="checkbox edit_sample_checkbox" value="">'
       }
     },
     {
@@ -42,7 +42,7 @@ build_columns = function() {
         if (data.value == null) {
             return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=6 maxlength=6>'
         } else {
-            return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id) - 1] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id) - 1] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
+            return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id) - 1] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id) - 1] + '" name="value:' + data.name + '" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
         }
       }
     }
@@ -66,9 +66,9 @@ build_columns = function() {
         'data': null,
         'render': function(data, type, row, meta) {
           if (data.variance == null) {
-              return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="x" size=6 maxlength=6>'
+              return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_se" value="x" size=6 maxlength=6>'
           } else {
-              return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>'
+              return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>'
           }
         }
       }
@@ -84,9 +84,9 @@ build_columns = function() {
         'data': null,
         'render': function(data, type, row, meta) {
           if (data.num_cases == null || data.num_cases == undefined) {
-              return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>'
+              return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>'
           } else {
-              return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>'
+              return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>'
           }
         }
       }
-- 
cgit v1.2.3