Moved SampleList to its own file and eliminated the +/- and SE columns when there are no SE values

3 files changed, 187 insertions, 170 deletions

diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py
index 0f21a958..92d0feaf 100755
--- a/wqflask/wqflask/show_trait/DataEditingPage.py
+++ b/wqflask/wqflask/show_trait/DataEditingPage.py
@@ -5,12 +5,13 @@ import os
 import cPickle
 #import pyXLWriter as xl
 
-import yaml
+from collections import OrderedDict
 
 from htmlgen import HTMLgen2 as HT
 
 from base import webqtlConfig
 from base import webqtlCaseData
+from wqflask.show_trait.SampleList import SampleList
 from utility import webqtlUtil, Plot, Bunch
 from base.webqtlTrait import webqtlTrait
 from dbFunction import webqtlDatabaseFunction
@@ -1514,171 +1515,3 @@ class DataEditingPage(templatePage):
         #        or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))):
         #    print("hjs")
         fd.allsamplelist = all_samples_ordered
-
-class SampleList(object):
-    def __init__(self,
-                 cursor,
-                 fd,
-                 variance_data_page,
-                 sample_names,
-                 this_trait,
-                 sample_group_type,
-                 header):
-        
-        self.cursor = cursor
-        self.fd = fd
-        self.this_trait = this_trait
-        self.sample_group_type = sample_group_type    # primary or other
-        self.header = header
-
-        self.sample_list = [] # The actual list
-        
-        self.calc_attributes()
-        
-        print("camera: attributes are:", pf(self.attributes))
-
-        for counter, sample_name in enumerate(sample_names, 1):
-            sample_name = sample_name.replace("_2nd_", "")
-
-            #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:
-                print("No sample %s, let's create it now" % sample_name)
-                sample = webqtlCaseData.webqtlCaseData(sample_name)
-            
-            #sampleNameAdd = ''
-            #if fd.RISet == 'AXBXA' and sampleName in ('AXB18/19/20','AXB13/14','BXA8/17'):
-            #    sampleNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank")
-            sample.extra_info = {}
-            if self.fd.RISet == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'):   
-                sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
-                sample.extra_info['css_class'] = "fs12" 
-
-            print("  type of sample:", type(sample))
-
-            if sample_group_type == 'primary':
-                sample.this_id = "Primary_" + str(counter)
-            else:
-                sample.this_id = "Other_" + str(counter)
-
-            #### For extra attribute columns; currently only used by several datasets - Zach
-            if self.this_trait and self.this_trait.db and self.this_trait.db.type == 'ProbeSet':
-                sample.extra_attributes = self.get_extra_attribute_values(sample_name)
-                print("sample.extra_attributes is", pf(sample.extra_attributes))
-                self.sample_list.append(sample)
-
-        print("self.attributes is", pf(self.attributes))
-
-        self.do_outliers()
-        #do_outliers(the_samples)
-        print("*the_samples are [%i]: %s" % (len(self.sample_list), pf(self.sample_list)))
-        for sample in self.sample_list:
-            print("apple:", type(sample), sample)
-        #return the_samples
-
-    def __repr__(self):
-        return "<SampleList> --> %s" % (pf(self.__dict__))
-
-    def do_outliers(self):
-        values = [sample.value for sample in self.sample_list if sample.value != None]
-        upper_bound, lower_bound = Plot.find_outliers(values)
-        
-        for sample in self.sample_list:
-            if sample.value:
-                if upper_bound and sample.value > upper_bound:
-                    sample.outlier = True
-                elif lower_bound and sample.value < lower_bound:
-                    sample.outlier = True
-                else:
-                    sample.outlier = False
-                    
-                    
-    def calc_attributes(self):
-        """Finds which extra attributes apply to this dataset"""
-        
-        #ZS: Id and name values for this trait's extra attributes  
-        self.cursor.execute('''SELECT CaseAttribute.Id, CaseAttribute.Name
-                                        FROM CaseAttribute, CaseAttributeXRef
-                                        WHERE CaseAttributeXRef.ProbeSetFreezeId = %s AND
-                                            CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId
-                                                group by CaseAttributeXRef.CaseAttributeId''',
-                                                (str(self.this_trait.db.id),))
-
-        
-        self.attributes = {}
-        for key, value in self.cursor.fetchall():
-            print("radish: %s - %s" % (key, value))
-            self.attributes[key] = Bunch()
-            self.attributes[key].name = value
-
-            self.cursor.execute('''SELECT DISTINCT CaseAttributeXRef.Value
-                            FROM CaseAttribute, CaseAttributeXRef
-                            WHERE CaseAttribute.Name = %s AND
-                                CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id''', (value,))            
-
-            self.attributes[key].distinct_values = [item[0] for item in self.cursor.fetchall()]
-            self.attributes[key].distinct_values.sort(key=natural_sort_key)
-
-
-        #    exclude_menu = HT.Select(name="exclude_menu")
-        #    dropdown_menus = [] #ZS: list of dropdown menus with the distinct values of each attribute (contained in DIVs so the style parameter can be edited and they can be hidden) 
-        #    for this_attr_name in attribute_names:
-        #        exclude_menu.append((this_attr_name.capitalize(), this_attr_name))
-        #        attr_value_menu_div = HT.Div(style="display:none;", Class="attribute_values") #container used to show/hide dropdown menus
-        #        attr_value_menu = HT.Select(name=this_attr_name)
-        #                    attr_value_menu.append(("None", "show_all"))
-        #        for value in distinct_values:
-        #            attr_value_menu.append((str(value[0]), value[0]))
-        #        attr_value_menu_div.append(attr_value_menu)
-        #        dropdown_menus.append(attr_value_menu_div)
-
-                    
-    def get_extra_attribute_values(self, sample_name):
-        
-        attribute_values = {}
-        
-        if self.attributes:
-
-            #ZS: Get StrainId value for the next query
-            self.cursor.execute("""SELECT Strain.Id
-                                        FROM Strain, StrainXRef, InbredSet
-                                        WHERE Strain.Name = %s and
-                                            StrainXRef.StrainId = Strain.Id and
-                                            InbredSet.Id = StrainXRef.InbredSetId and
-                                            InbredSet.Name = %s""", (sample_name, self.fd.RISet))
-
-            sample_id = self.cursor.fetchone()[0]
-
-            for attribute in self.attributes:
-
-                #ZS: Add extra case attribute values (if any)
-                self.cursor.execute("""SELECT Value
-                                                FROM CaseAttributeXRef
-                                        WHERE ProbeSetFreezeId = '%s' AND
-                                                StrainId = '%s' AND
-                                                CaseAttributeId = '%s'
-                                        group by CaseAttributeXRef.CaseAttributeId""" % (
-                                            self.this_trait.db.id, sample_id, str(attribute)))
-
-                attribute_value = self.cursor.fetchone()[0] #Trait-specific attributes, if any
-
-                #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:
-                    pass
-                
-                attribute_values[self.attributes[attribute].name] = attribute_value
-               
-        return attribute_values
-
-
-def natural_sort_key(x):
-    """Get expected results when using as a key for sort - ints or strings are sorted properly"""
-    try:
-        x = int(x)
-    except ValueError:
-        pass
-    return x
\ No newline at end of file
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
new file mode 100644
index 00000000..62bc63c3
--- /dev/null
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -0,0 +1,181 @@
+from __future__ import absolute_import, print_function, division
+
+from base import webqtlCaseData
+from utility import webqtlUtil, Plot, Bunch
+from base.webqtlTrait import webqtlTrait
+
+from pprint import pformat as pf
+
+class SampleList(object):
+    def __init__(self,
+                 cursor,
+                 fd,
+                 variance_data_page,
+                 sample_names,
+                 this_trait,
+                 sample_group_type,
+                 header):
+        
+        self.cursor = cursor
+        self.fd = fd
+        self.this_trait = this_trait
+        self.sample_group_type = sample_group_type    # primary or other
+        self.header = header
+
+        self.sample_list = [] # The actual list
+        
+        self.calc_attributes()
+        
+        print("camera: attributes are:", pf(self.attributes))
+
+        for counter, sample_name in enumerate(sample_names, 1):
+            sample_name = sample_name.replace("_2nd_", "")
+
+            #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:
+                print("No sample %s, let's create it now" % sample_name)
+                sample = webqtlCaseData.webqtlCaseData(sample_name)
+            
+            #sampleNameAdd = ''
+            #if fd.RISet == 'AXBXA' and sampleName in ('AXB18/19/20','AXB13/14','BXA8/17'):
+            #    sampleNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank")
+            sample.extra_info = {}
+            if self.fd.RISet == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'):   
+                sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
+                sample.extra_info['css_class'] = "fs12" 
+
+            print("  type of sample:", type(sample))
+
+            if sample_group_type == 'primary':
+                sample.this_id = "Primary_" + str(counter)
+            else:
+                sample.this_id = "Other_" + str(counter)
+
+            #### For extra attribute columns; currently only used by several datasets - Zach
+            if self.this_trait and self.this_trait.db and self.this_trait.db.type == 'ProbeSet':
+                sample.extra_attributes = self.get_extra_attribute_values(sample_name)
+                print("sample.extra_attributes is", pf(sample.extra_attributes))
+                self.sample_list.append(sample)
+
+        print("self.attributes is", pf(self.attributes))
+
+        self.do_outliers()
+        #do_outliers(the_samples)
+        print("*the_samples are [%i]: %s" % (len(self.sample_list), pf(self.sample_list)))
+        for sample in self.sample_list:
+            print("apple:", type(sample), sample)
+        #return the_samples
+
+    def __repr__(self):
+        return "<SampleList> --> %s" % (pf(self.__dict__))
+
+    def do_outliers(self):
+        values = [sample.value for sample in self.sample_list if sample.value != None]
+        upper_bound, lower_bound = Plot.find_outliers(values)
+        
+        for sample in self.sample_list:
+            if sample.value:
+                if upper_bound and sample.value > upper_bound:
+                    sample.outlier = True
+                elif lower_bound and sample.value < lower_bound:
+                    sample.outlier = True
+                else:
+                    sample.outlier = False
+                    
+                    
+    def calc_attributes(self):
+        """Finds which extra attributes apply to this dataset"""
+        
+        #ZS: Id and name values for this trait's extra attributes  
+        self.cursor.execute('''SELECT CaseAttribute.Id, CaseAttribute.Name
+                                        FROM CaseAttribute, CaseAttributeXRef
+                                        WHERE CaseAttributeXRef.ProbeSetFreezeId = %s AND
+                                            CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId
+                                                group by CaseAttributeXRef.CaseAttributeId''',
+                                                (str(self.this_trait.db.id),))
+
+
+        self.attributes = {}
+        for key, value in self.cursor.fetchall():
+            print("radish: %s - %s" % (key, value))
+            self.attributes[key] = Bunch()
+            self.attributes[key].name = value
+
+            self.cursor.execute('''SELECT DISTINCT CaseAttributeXRef.Value
+                            FROM CaseAttribute, CaseAttributeXRef
+                            WHERE CaseAttribute.Name = %s AND
+                                CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id''', (value,))            
+
+            self.attributes[key].distinct_values = [item[0] for item in self.cursor.fetchall()]
+            self.attributes[key].distinct_values.sort(key=natural_sort_key)
+
+
+        #    exclude_menu = HT.Select(name="exclude_menu")
+        #    dropdown_menus = [] #ZS: list of dropdown menus with the distinct values of each attribute (contained in DIVs so the style parameter can be edited and they can be hidden) 
+        #    for this_attr_name in attribute_names:
+        #        exclude_menu.append((this_attr_name.capitalize(), this_attr_name))
+        #        attr_value_menu_div = HT.Div(style="display:none;", Class="attribute_values") #container used to show/hide dropdown menus
+        #        attr_value_menu = HT.Select(name=this_attr_name)
+        #                    attr_value_menu.append(("None", "show_all"))
+        #        for value in distinct_values:
+        #            attr_value_menu.append((str(value[0]), value[0]))
+        #        attr_value_menu_div.append(attr_value_menu)
+        #        dropdown_menus.append(attr_value_menu_div)
+
+                    
+    def get_extra_attribute_values(self, sample_name):
+
+        attribute_values = {}
+
+        if self.attributes:
+
+            #ZS: Get StrainId value for the next query
+            self.cursor.execute("""SELECT Strain.Id
+                                        FROM Strain, StrainXRef, InbredSet
+                                        WHERE Strain.Name = %s and
+                                            StrainXRef.StrainId = Strain.Id and
+                                            InbredSet.Id = StrainXRef.InbredSetId and
+                                            InbredSet.Name = %s""", (sample_name, self.fd.RISet))
+
+            sample_id = self.cursor.fetchone()[0]
+
+            for attribute in self.attributes:
+
+                #ZS: Add extra case attribute values (if any)
+                self.cursor.execute("""SELECT Value
+                                                FROM CaseAttributeXRef
+                                        WHERE ProbeSetFreezeId = '%s' AND
+                                                StrainId = '%s' AND
+                                                CaseAttributeId = '%s'
+                                        group by CaseAttributeXRef.CaseAttributeId""" % (
+                                            self.this_trait.db.id, sample_id, str(attribute)))
+
+                attribute_value = self.cursor.fetchone()[0] #Trait-specific attributes, if any
+
+                #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:
+                    pass
+                
+                attribute_values[self.attributes[attribute].name] = attribute_value
+               
+        return 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"""
+    
+    try:
+        x = int(x)
+    except ValueError:
+        pass
+    return x        
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html
index f227d780..7d0e671f 100644
--- a/wqflask/wqflask/templates/trait_data_and_analysis.html
+++ b/wqflask/wqflask/templates/trait_data_and_analysis.html
@@ -1259,10 +1259,11 @@
                               <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="100">Sample</th>
 
                               <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="70">Value</th>
-
+                              {% if sample_type.se_exists() %}
                               <th class="fs13 fwb ff1 b1 cw cbrb" width="20">&nbsp;</th>
 
                               <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="80">SE</th>
+                              {% endif %}
                               
                               {% for attribute in sample_type.attributes|sort() %}
                                 <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="60">{{ sample_type.attributes[attribute].name }}</th>
@@ -1287,6 +1288,7 @@
                                        style="text-align:right; background-color:#FFFFFF;">
                               </td>
 
+                              {% if sample_type.se_exists() %}
                               <td class="fs13 b1 c222" align="center" width="20">
                                 ±
                               </td>
@@ -1297,6 +1299,7 @@
                                        value="{{ sample.display_variance }}"
                                        size="8" maxlength="8" style="text-align:right">
                               </td>
+                              {% endif %}
                               
                               {# Loop through each attribute type and input value #}
                               {% for attribute in sample_type.attributes|sort() %}