Added minimum/maximum to basic statistics table

Continued bug-shooting related to getting show_trait running
with phenotype traits

12 files changed, 122 insertions, 84 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 9f0f3fac..2182fe9e 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -30,6 +30,7 @@ from htmlgen import HTMLgen2 as HT
 import reaper
 
 import webqtlConfig
+from dbFunction import webqtlDatabaseFunction
 from utility import webqtlUtil
 
 from MySQLdb import escape_string as escape
@@ -72,10 +73,12 @@ class DatasetGroup(object):
     """
     def __init__(self, dataset):
         """This sets self.group and self.group_id"""
-        self.name, self.group_id = g.db.execute(dataset.query).fetchone()
+        self.name, self.id = g.db.execute(dataset.query_for_group).fetchone()
         if self.name == 'BXD300':
             self.name = "BXD"
         
+        self.species = webqtlDatabaseFunction.retrieve_species(self.name)
+        
         self.incparentsf1 = False
         self.f1list = None
         self.parlist = None
@@ -151,14 +154,25 @@ class DataSet(object):
 
         self.check_confidentiality()
 
-        self.retrieve_name()
+        self.retrieve_other_names()
         self.group = DatasetGroup(self)   # sets self.group and self.group_id
        
         
     def get_desc(self):
         """Gets overridden later, at least for Temp...used by trait's get_given_name"""
         return None
-
+    
+    #@staticmethod
+    #def get_by_trait_id(trait_id):
+    #    """Gets the dataset object given the trait id"""
+    #    
+    #    
+    #
+    #    name = g.db.execute(""" SELECT 
+    #                        
+    #                        """)
+    #    
+    #    return DataSet(name)
 
     # Delete this eventually
     @property
@@ -175,7 +189,7 @@ class DataSet(object):
 
 
 
-    def retrieve_name(self):
+    def retrieve_other_names(self):
         """
         If the data set name parameter is not found in the 'Name' field of the data set table,
         check if it is actually the FullName or ShortName instead.
@@ -326,7 +340,7 @@ class PhenotypeDataSet(DataSet):
     def retrieve_sample_data(self, trait):
         query = """
                     SELECT
-                            Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id
+                            Strain.Name, PublishData.value, PublishSE.error, NStrain.count
                     FROM
                             (PublishData, Strain, PublishXRef, PublishFreeze)
                     left join PublishSE on
@@ -340,7 +354,7 @@ class PhenotypeDataSet(DataSet):
                             PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id
                     Order BY
                             Strain.Name
-                    """ % (self.trait.name, self.id)
+                    """ % (trait.name, self.id)
         results = g.db.execute(query).fetchall()
         return results
 
@@ -368,7 +382,7 @@ class GenotypeDataSet(DataSet):
         # Todo: Obsolete or rename this field
         self.type = 'Geno'
 
-        self.query = '''
+        self.query_for_group = '''
                 SELECT
                         InbredSet.Name, InbredSet.Id
                 FROM
@@ -418,7 +432,7 @@ class GenotypeDataSet(DataSet):
                             GenoData.StrainId = Strain.Id
                     Order BY
                             Strain.Name
-                    """ % (webqtlDatabaseFunction.retrieve_species_id(self.group), trait.name, self.name)
+                    """ % (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait.name, self.name)
         results = g.db.execute(query).fetchall()
         return results
 
@@ -476,7 +490,7 @@ class MrnaAssayDataSet(DataSet):
         # Todo: Obsolete or rename this field
         self.type = 'ProbeSet'
 
-        self.query = '''
+        self.query_for_group = '''
                         SELECT
                                 InbredSet.Name, InbredSet.Id
                         FROM
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 69602748..403f1b5e 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -177,9 +177,6 @@ class PhenotypeSearch(DoSearch):
 
         from_clause = self.normalize_spaces(from_clause)
 
-        #Get group information for dataset
-        self.dataset.get_group()
-
         query = (self.base_query +
                 """%s
                     WHERE %s
@@ -189,7 +186,7 @@ class PhenotypeSearch(DoSearch):
                     PublishFreeze.Id = %s""" % (
                         from_clause,
                         where_clause,
-                        escape(str(self.dataset.group_id)),
+                        escape(str(self.dataset.group.id)),
                         escape(str(self.dataset.id))))
 
         print("query is:", pf(query))
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index b518ab99..5cb8e314 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -4,13 +4,6 @@ from wqflask import app
 
 from flask import render_template
 
-###################################################
-#                                                 #
-# This file uses only spaces for indentation      #
-#                                                 #
-###################################################
-
-#import string
 import os
 import cPickle
 import re
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index cd61d70c..d1c60877 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -32,13 +32,16 @@ from pprint import pformat as pf
 
 
 
-class ShowTrait(templatePage):
+class ShowTrait(object):
 
     def __init__(self, args):
         print("in ShowTrait, args are:", args)
         #self.group = args.group
         self.trait_id = args['trait_id']
+        
         self.dataset = create_dataset(args['dataset'])
+        
+        #self.dataset = create_dataset(args['dataset'])
         self.cell_id = None
 
         #assert self.openMysql(), "No database!"
@@ -817,7 +820,7 @@ class ShowTrait(templatePage):
                 #        ))
                 pass
 
-            menuTable = HT.TableLite(cellpadding=2, Class="collap", width="150", id="target1")
+            #menuTable = HT.TableLite(cellpadding=2, Class="collap", width="150", id="target1")
             #menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
             #menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
 
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index 6e22119f..3d9fcd5a 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -23,15 +23,15 @@ $ ->
         id = "#" + process_id(category, value_type)
         console.log("the_id:", id)
         in_box = $(id).html
-        
+
         current_value = parseFloat($(in_box)).toFixed(decimal_places)
-        
+
         console.log("urgh:", category, value_type)
         the_value = sample_sets[category][value_type]()
         console.log("After running sample_sets, the_value is:", the_value)
         if decimal_places > 0
             the_value = the_value.toFixed(decimal_places)
-        
+
         console.log("*-* the_value:", the_value)
         console.log("*-* current_value:", current_value)
         if the_value != current_value
@@ -40,16 +40,16 @@ $ ->
     update_stat_values = (sample_sets)->
         for category in ['samples_primary', 'samples_other', 'samples_all']
             change_stats_value(sample_sets, category, "n_of_samples", 0)
-            for stat in ["mean", "median", "std_dev", "std_error"]
+            for stat in ["mean", "median", "std_dev", "std_error", "min", "max"]
                 console.log("Calling change_stats_value")
                 change_stats_value(sample_sets, category, stat, 2)
 
-    edit_data_change = ->                
+    edit_data_change = ->
         sample_sets =
             samples_primary: new Stats([])
             samples_other: new Stats([])
             samples_all: new Stats([])
-                
+
         console.log("at beginning:", sample_sets)
 
         # ##########
@@ -114,6 +114,14 @@ $ ->
                 {
                     vn: "std_dev"
                     pretty: "Standard Deviation (SD)"
+                },
+                {
+                    vn: "min"
+                    pretty: "Minimum"
+                },
+                {
+                    vn: "max"
+                    pretty: "Maximum"
                 }
         ]
 
@@ -150,8 +158,8 @@ $ ->
                 processed += "-"
             processed += value
         return processed
-    
-    
+
+
     show_hide_outliers = ->
         console.log("FOOBAR in beginning of show_hide_outliers")
         label = $('#show_hide_outliers').val()
@@ -163,10 +171,10 @@ $ ->
             $('#show_hide_outliers').val("Hide Outliers")
             console.log("Should be now Hide Outliers")
 
-    
+
     ##Calculate Correlations Code
-    
-    
+
+
     on_corr_method_change = ->
         console.log("in beginning of on_corr_method_change")
         corr_method = $('select[name=corr_method]').val()
@@ -179,15 +187,15 @@ $ ->
             $("#corr_sample_method_options").show()
 
     $('select[name=corr_method]').change(on_corr_method_change)
-    
-    
+
+
     ##End Calculate Correlations Code
-    
+
     ##Populate Samples Attribute Values Code
-    
+
     create_value_dropdown = (value) ->
         return """<option val=#{value}>#{value}</option>"""
-    
+
     populate_sample_attributes_values_dropdown = ->
         console.log("in beginning of psavd")
         $('#attribute_values').empty()
@@ -205,14 +213,14 @@ $ ->
     if js_data.attribute_names.length > 0
         populate_sample_attributes_values_dropdown()
     $('#exclude_menu').change(populate_sample_attributes_values_dropdown)
-    
+
     ##End Populate Samples Attribute Values Codess
 
     ##Block Samples By Attribute Value Code
     block_by_attribute_value = ->
         attribute_name = $('#exclude_menu').val()
         exclude_by_value = $('#attribute_values').val()
-        
+
         cell_class = ".column_name-#{attribute_name}"
         $(cell_class).each (index, element) =>
             if $.trim($(element).text()) == exclude_by_value
@@ -220,11 +228,11 @@ $ ->
                 $(row).find(".trait_value_input").val("x")
 
     $('#exclude_group').click(block_by_attribute_value)
-    
+
     ##End Block Samples By Attribute Value Code
-    
+
     ##Block Samples By Index Code
-    
+
     block_by_index = ->
         index_string = $('#remove_samples_field').val()
         index_list = []
@@ -241,7 +249,7 @@ $ ->
                     index = parseInt(index_set)
                     console.log("index:", index)
                     index_list.push(index)
-                #catch(erro) 
+                #catch(erro)
                 #    alert("Syntax error")
         console.log("index_list:", index_list)
         for index in index_list
@@ -251,33 +259,33 @@ $ ->
                 $('#Primary_'+index.toString()).find('.trait_value_input').val("x")
             else if $('#block_group').val() == "other"
                 console.log("block_group:", $('#block_group').val())
-                console.log("row:", $('#Other_'+index.toString()))                
+                console.log("row:", $('#Other_'+index.toString()))
                 $('#Other_'+index.toString()).find('.trait_value_input').val("x")
-    
+
     $('#block_by_index').click(block_by_index)
 
     ##End Block Samples By Index Code
-    
+
     ##Hide Sample Rows With No Value (value of 'x') Code
-    
+
     hide_no_value = ->
         $('.value_se').each (_index, element) =>
             if $(element).find('.trait_value_input').val() == 'x'
                 $(element).hide()
-                
+
     $('#hide_no_value').click(hide_no_value)
 
     ##End Hide Sample Rows With No Value Code
-    
+
     ##Block Outliers Code
     block_outliers = ->
         $('.outlier').each (_index, element) =>
             $(element).find('.trait_value_input').val('x')
-            
+
     $('#block_outliers').click(block_outliers)
-    
+
     ##End Block Outliers Code
-    
+
     ##Reset Table Values Code
     reset_samples_table = ->
         $('.trait_value_input').each (_index, element) =>
@@ -289,9 +297,9 @@ $ ->
     $('#reset').click(reset_samples_table)
 
     ##End Reset Table Values Code
-    
+
     ##Get Sample Data From Table Code
-    
+
     get_sample_table_data = ->
         samples = {}
         primary_samples = []
@@ -315,27 +323,27 @@ $ ->
     ##End Get Sample Data from Table Code
 
     ##Export Sample Table Data Code
-    
+
     export_sample_table_data = ->
         sample_data = get_sample_table_data()
         console.log("sample_data is:", sample_data)
         json_sample_data = JSON.stringify(sample_data)
         console.log("json_sample_data is:", json_sample_data)
-        
+
         $('input[name=export_data]').val(json_sample_data)
         console.log("export_data is", $('input[name=export_data]').val())
-        
+
         format = $('#export_format').val()
         if format == "excel"
             $('#trait_data_form').attr('action', '/export_trait_excel')
         else
             $('#trait_data_form').attr('action', '/export_trait_csv')
         console.log("action is:", $('#trait_data_form').attr('action'))
-        
+
         $('#trait_data_form').submit()
 
     $('#export').click(export_sample_table_data)
-    
+
     ##End Export Sample Table Data Code
 
 
@@ -344,7 +352,7 @@ $ ->
     console.log("after registering block_outliers")
 
     _.mixin(_.str.exports());  # Add string fuctions directly to underscore
-    $('#value_table').change(edit_data_change)
+    $('#edit_sample_lists').change(edit_data_change)
     console.log("loaded")
     #console.log("basic_table is:", basic_table)
     # Add back following two lines later
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 919bc766..84282aef 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -53,7 +53,7 @@
         change_stats_value(sample_sets, category, "n_of_samples", 0);
         _results.push((function() {
           var _j, _len1, _ref1, _results1;
-          _ref1 = ["mean", "median", "std_dev", "std_error"];
+          _ref1 = ["mean", "median", "std_dev", "std_error", "min", "max"];
           _results1 = [];
           for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) {
             stat = _ref1[_j];
@@ -126,6 +126,12 @@
         }, {
           vn: "std_dev",
           pretty: "Standard Deviation (SD)"
+        }, {
+          vn: "min",
+          pretty: "Minimum"
+        }, {
+          vn: "max",
+          pretty: "Maximum"
         }
       ];
       console.log("rows are:", rows);
@@ -362,7 +368,7 @@
     $('#block_outliers').click(block_outliers);
     console.log("after registering block_outliers");
     _.mixin(_.str.exports());
-    $('#value_table').change(edit_data_change);
+    $('#edit_sample_lists').change(edit_data_change);
     console.log("loaded");
     make_table();
     edit_data_change();
diff --git a/wqflask/wqflask/static/new/javascript/stats.coffee b/wqflask/wqflask/static/new/javascript/stats.coffee
index 677dc258..118ee7a8 100644
--- a/wqflask/wqflask/static/new/javascript/stats.coffee
+++ b/wqflask/wqflask/static/new/javascript/stats.coffee
@@ -1,20 +1,20 @@
 class Stats
     constructor: (@the_values) ->
-        
+
     add_value: (value) ->
         @the_values.push(value)
-    
+
     n_of_samples: ->
         return @the_values.length
-        
+
     sum: ->
         total = 0
         total += value for value in @the_values
         return total
-    
+
     mean: ->
         return @sum() / @n_of_samples()
-    
+
     median: ->
         is_odd = @the_values.length % 2
         median_position = Math.floor(@the_values.length / 2)
@@ -24,7 +24,7 @@ class Stats
         else
             return (the_values_sorted[median_position] +
                     the_values_sorted[median_position - 1]) / 2
-        
+
     std_dev: ->
         sum = 0
         for value in @the_values
@@ -32,15 +32,22 @@ class Stats
             sum += step_a
         step_b = sum / @the_values.length
         return Math.sqrt(step_b)
-    
+
     std_error: ->
         return @std_dev() / Math.sqrt(@n_of_samples())
 
+    min: ->
+        return Math.min(@the_values...)
+
+    max: ->
+        return Math.max(@the_values...)
+
 
 bxd_only = new Stats([3, 5, 7, 8])
-console.log("[red] bxd_only mean:", bxd_only.mean())
-console.log("[green] bxd_only median:", bxd_only.median())
-console.log("[purple] bxd_only std_dev:", bxd_only.std_dev())
-console.log("[magenta] bxd_only std_error:", bxd_only.std_error())
+console.log("[xred] bxd_only mean:", bxd_only.mean())
+console.log("[xgreen] bxd_only median:", bxd_only.median())
+console.log("[xpurple] bxd_only std_dev:", bxd_only.std_dev())
+console.log("[xmagenta] bxd_only std_error:", bxd_only.std_error())
+console.log("[xyellow] bxd_only min:", bxd_only.min())
 
-window.Stats = Stats
\ No newline at end of file
+window.Stats = Stats
diff --git a/wqflask/wqflask/static/new/javascript/stats.js b/wqflask/wqflask/static/new/javascript/stats.js
index f95d03d4..620f7d5d 100644
--- a/wqflask/wqflask/static/new/javascript/stats.js
+++ b/wqflask/wqflask/static/new/javascript/stats.js
@@ -62,19 +62,29 @@
       return this.std_dev() / Math.sqrt(this.n_of_samples());
     };
 
+    Stats.prototype.min = function() {
+      return Math.min.apply(Math, this.the_values);
+    };
+
+    Stats.prototype.max = function() {
+      return Math.max.apply(Math, this.the_values);
+    };
+
     return Stats;
 
   })();
 
   bxd_only = new Stats([3, 5, 7, 8]);
 
-  console.log("[red] bxd_only mean:", bxd_only.mean());
+  console.log("[xred] bxd_only mean:", bxd_only.mean());
+
+  console.log("[xgreen] bxd_only median:", bxd_only.median());
 
-  console.log("[green] bxd_only median:", bxd_only.median());
+  console.log("[xpurple] bxd_only std_dev:", bxd_only.std_dev());
 
-  console.log("[purple] bxd_only std_dev:", bxd_only.std_dev());
+  console.log("[xmagenta] bxd_only std_error:", bxd_only.std_error());
 
-  console.log("[magenta] bxd_only std_error:", bxd_only.std_error());
+  console.log("[xyellow] bxd_only min:", bxd_only.min());
 
   window.Stats = Stats;
 
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 35ff4e8e..11f68bba 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -51,9 +51,9 @@
                         </TD>
                         <TD>
                             <a href="{{ url_for('show_trait_page',
-                                    dataset = dataset.name,
                                     trait_id = this_trait.name,
-                                    group = dataset.group)}}">
+                                    dataset = dataset.name
+                                    )}}">
                                 {{ this_trait.name }}
                             </a>
                         </TD>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 163be69c..28341186 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -18,7 +18,7 @@
 
         <div class="container">
             <div class="page-header">
-                <h1>{{ this_trait.species.capitalize() }} -
+                <h1>{{ dataset.group.species.capitalize() }} -
                     {{ dataset.group.name }} -
                     {{ this_trait.symbol }}
                 </h1>
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index e45886b4..e04fdd66 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -8,7 +8,7 @@
     <dt>Database</dt>
     <dd>
         <a href="{{ this_trait.database.url }}" target="_blank">
-            {{ this_trait.database.name }}
+            {{ dataset.name }}
         </a>
     </dd>
 
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 6c9b1073..9023b34d 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -77,7 +77,7 @@
         <table id="stats_table" class="table table-hover"></table>
     </div>
 
-    <div>
+    <div id="edit_sample_lists">
     {% for sample_type in sample_groups %}
         <div>
             <h3>{{ sample_type.header }}</h3>