Wrote coffeescript for the functions Hide No Value, Reset, and Hide Outliers

Added data attribute to input fields to store the original value for the Reset function

Began replacing search_results.py parsing code with parser.py's parse function

6 files changed, 128 insertions, 231 deletions

diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py
index 16eff609..53df2001 100644
--- a/wqflask/wqflask/parser.py
+++ b/wqflask/wqflask/parser.py
@@ -25,7 +25,7 @@ def parse(pstring):
                 assert value.endswith(")"), "Invalid token"
                 value = value[1:-1] # Get rid of the parenthesis
                 values = re.split(r"""\s+|,""", value)
-                value = [value.strip() for value in values]
+                value = [value.strip() for value in values if value.strip()]
             term = dict(key=key,
                         seperator=seperator,
                         value=value)
@@ -33,9 +33,13 @@ def parse(pstring):
             term = dict(search_term = item)
             
         items.append(term)
-    print(pf(items))
+    #print(pf(items))
+    return(items)
     
 parse("foo=(3 2 1)")
+parse("shh")
+parse("shh grep")
 parse("LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)")
 parse("sal1 LRS=(9 99 Chr4 122 155) sal2 cisLRS=(9 999 10)")
-parse("sal1 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9 999 10)")
\ No newline at end of file
+parse("sal1 sal3 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9 999 10)")
+parse("sal1 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9, 999, 10)")
\ No newline at end of file
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 3c54be3c..6847c369 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -32,6 +32,7 @@ from utility.TDCell import TDCell
 from base.webqtlDataset import webqtlDataset
 from base.webqtlTrait import webqtlTrait
 from base.templatePage import templatePage
+from wqflask import parser
 from utility import webqtlUtil
 from dbFunction import webqtlDatabaseFunction
 
@@ -597,28 +598,35 @@ class SearchResultPage(templatePage):
 
 
     def normalSearch(self):
-        self.ANDkeyword2 = re.sub(self._1mPattern, '', self.ANDkeyword)
-        self.ANDkeyword2 = re.sub(self._2mPattern, '', self.ANDkeyword2)
-        self.ANDkeyword2 = re.sub(self._3mPattern, '', self.ANDkeyword2)
-        self.ANDkeyword2 = re.sub(self._5mPattern, '', self.ANDkeyword2)
-        ##remove remain parethesis, could be input with  syntax error
-        self.ANDkeyword2 = re.sub(re.compile('\s*\([\s\S]*\)'), '', self.ANDkeyword2)
-        self.ANDkeyword2 = self.encregexp(self.ANDkeyword2)
-
-        self.ORkeyword2 = re.sub(self._1mPattern, '', self.ORkeyword)
-        self.ORkeyword2 = re.sub(self._2mPattern, '', self.ORkeyword2)
-        self.ORkeyword2 = re.sub(self._3mPattern, '', self.ORkeyword2)
-        self.ORkeyword2 = re.sub(self._5mPattern, '', self.ORkeyword2)
-        ##remove remain parethesis, could be input with  syntax error
-        self.ORkeyword2 = re.sub(re.compile('\s*\([\s\S]*\)'), '', self.ORkeyword2)
-        self.ORkeyword2 = self.encregexp(self.ORkeyword2)
+        print("ORkeyword is:", pf(self.ORkeyword))
+        self.ANDkeyword2 = parser.parse(self.ANDkeyword)
+        self.ORkeyword2 = parser.parse(self.ORkeyword)
+        print("ORkeyword2 is:", pf(parser.parse(self.ORkeyword)))
+        
+        #self.ANDkeyword2 = re.sub(self._1mPattern, '', self.ANDkeyword)
+        #self.ANDkeyword2 = re.sub(self._2mPattern, '', self.ANDkeyword2)
+        #self.ANDkeyword2 = re.sub(self._3mPattern, '', self.ANDkeyword2)
+        #self.ANDkeyword2 = re.sub(self._5mPattern, '', self.ANDkeyword2)
+        ###remove remain parethesis, could be input with  syntax error
+        #self.ANDkeyword2 = re.sub(re.compile('\s*\([\s\S]*\)'), '', self.ANDkeyword2)
+        #self.ANDkeyword2 = self.encregexp(self.ANDkeyword2)
+        #
+        #self.ORkeyword2 = re.sub(self._1mPattern, '', self.ORkeyword)
+        #self.ORkeyword2 = re.sub(self._2mPattern, '', self.ORkeyword2)
+        #self.ORkeyword2 = re.sub(self._3mPattern, '', self.ORkeyword2)
+        #self.ORkeyword2 = re.sub(self._5mPattern, '', self.ORkeyword2)
+        ###remove remain parethesis, could be input with  syntax error
+        #self.ORkeyword2 = re.sub(re.compile('\s*\([\s\S]*\)'), '', self.ORkeyword2)
+        #self.ORkeyword2 = self.encregexp(self.ORkeyword2)
 
         if self.ORkeyword2 or self.ANDkeyword2:
             ANDFulltext = []
             ORFulltext = []
             for k, item in enumerate(self.ORkeyword2 + self.ANDkeyword2):
+                item = item['search_term']
                 self.nkeywords += 1
-                if k >=len(self.ORkeyword2):
+                #ZS: If there are both AND and OR keywords, just use the OR keywords
+                if k >=len(self.ORkeyword2): 
                     query = self.ANDQuery
                     DescriptionText = self.ANDDescriptionText
                     clausejoin = ' OR '
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index d34ae9a6..9b47f658 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -146,7 +146,7 @@ class ShowTrait(templatePage):
 
 
         self.make_sample_lists(fd, variance_data_page, this_trait)
-        
+
         if fd.allsamplelist:
             hddn['allsamplelist'] = string.join(fd.allsamplelist, ' ')
 
@@ -182,7 +182,7 @@ class ShowTrait(templatePage):
         cell_id = self.fd.get('CellID')        
 
         this_trait =  webqtlTrait(db=database, name=probe_set_id, cellid=cell_id, cursor=self.cursor)
-    
+
         ##identification, etc.
         self.fd.identification = '%s : %s' % (this_trait.db.shortname, probe_set_id)
         this_trait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\
@@ -195,14 +195,12 @@ class ShowTrait(templatePage):
         this_trait.retrieveInfo()
         this_trait.retrieveData()
         return this_trait
-    
+
 
     def dispTraitInformation(self, fd, title1Body, hddn, this_trait):
 
         _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
 
-        #tbl = HT.TableLite(cellpadding=2, Class="collap", style="margin-left:20px;", width="840", valign="top", id="target1")
-
         #reset=HT.Input(type='Reset',name='',value=' Reset ',Class="button")
 
         #XZ, August 02, 2011: The display of icons is decided by the trait type (if trait exists), along with user log-in status. Note that the new submitted trait might not be trait object.
@@ -802,9 +800,12 @@ class ShowTrait(templatePage):
 
     def dispBasicStatistics(self, fd, this_trait):
 
-        #XZ, June 22, 2011: The definition and usage of primary_samples, other_samples, specialStrains, all_samples are not clear and hard to understand. But since they are only used in this function for draw graph purpose, they will not hurt the business logic outside. As of June 21, 2011, this function seems work fine, so no hurry to clean up. These parameters and code in this function should be cleaned along with fd.f1list, fd.parlist, fd.samplelist later.
-        #stats_row = HT.TR()
-        #stats_cell = HT.TD()
+        #XZ, June 22, 2011: The definition and usage of primary_samples, other_samples,
+        #specialStrains, all_samples are not clear and hard to understand. But since they are
+        #only used in this function for draw graph purpose, they will not hurt the business logic
+        #outside. As of June 21, 2011, this function seems work fine, so no hurry to clean up.
+        #These parameters and code in this function should be cleaned along with fd.f1list,
+        #fd.parlist, fd.samplelist later.
 
         if fd.genotype.type == "riset":
             samplelist = fd.f1list + fd.samplelist
@@ -816,7 +817,6 @@ class ShowTrait(templatePage):
         all_samples = []
         primary_samples = [] #XZ: sample of primary group, e.g., BXD, LXS
 
-        #self.MDP_menu = HT.Select(name='stats_mdp', Class='stats_mdp')
         self.MDP_menu = [] # We're going to use the same named data structure as in the old version
                       # but repurpose it for Jinja2 as an array
 
@@ -827,10 +827,15 @@ class ShowTrait(templatePage):
                     if sample.find('F1') < 0:
                         specialStrains.append(sample)
                     if (this_trait.data[sampleName].value != None) and (sample not in (fd.f1list + fd.parlist)):
-                        other_samples.append(sample) #XZ: at current stage, other_samples doesn't include parent samples and F1 samples of primary group
+                        #XZ: at current stage, other_samples doesn't include parent samples and
+                        #F1 samples of primary group
+                        other_samples.append(sample) 
             else:
                 if (this_trait.data[sampleName].value != None) and (sample not in (fd.f1list + fd.parlist)):
-                    primary_samples.append(sample) #XZ: at current stage, the primary_samples is the same as fd.samplelist / ZS: I tried defining primary_samples as fd.samplelist instead, but in some cases it ended up including the parent samples (1436869_at BXD)
+                    #XZ: at current stage, the primary_samples is the same as fd.samplelist
+                    #ZS: I tried defining primary_samples as fd.samplelist instead, but in some
+                    #cases it ended up including the parent samples (1436869_at BXD)
+                    primary_samples.append(sample) 
 
         if len(other_samples) > 3:
             other_samples.sort(key=webqtlUtil.natsort_key)
@@ -838,7 +843,6 @@ class ShowTrait(templatePage):
             primary_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_samples #XZ: note that fd.f1list and fd.parlist are added.
             all_samples = primary_samples + other_samples
             other_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + other_samples #XZ: note that fd.f1list and fd.parlist are added.
-            print("ac1")   # This is the one used for first sall3
             self.MDP_menu.append(('All Cases','0'))
             self.MDP_menu.append(('%s Only' % fd.RISet, '1'))
             self.MDP_menu.append(('Non-%s Only' % fd.RISet, '2'))
@@ -854,7 +858,6 @@ class ShowTrait(templatePage):
                 all_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + all_samples
                 primary_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_samples
             else:
-                print("ac3")
                 all_samples = samplelist
 
             other_samples.sort(key=webqtlUtil.natsort_key)
@@ -888,13 +891,6 @@ class ShowTrait(templatePage):
                 #    continue
 
                 vals1.append(thisValFull)
-                
-                
-            #vals1 = [[sampleNameOrig.replace("_2nd_", ""),
-            #  this_trait.data[sampleName].val,
-            #  this_trait.data[sampleName].var]
-            #    for sampleNameOrig in all_samples]]
-            #    
 
             #Using just the RISet sample
             for sampleNameOrig in primary_samples:
@@ -948,7 +944,6 @@ class ShowTrait(templatePage):
                 stats_container = HT.Div(id="stats_tabs", style="padding:10px;", Class="ui-tabs") #Needed for tabs; notice the "stats_script_text" below referring to this element
                 stats_container.append(HT.Div(HT.Italic("Fewer than 4 case data were entered. No statistical analysis has been attempted.")))
                 stats_script_text = """$(function() { $("#stats_tabs").tabs();});"""
-                #stats_cell.append(stats_container)
                 break
             elif (i == 1 and len(primary_samples) < 4):
                 stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs")
@@ -958,19 +953,11 @@ class ShowTrait(templatePage):
                 stats_container.append(HT.Div(HT.Italic("Fewer than 4 non-" + fd.RISet + " case data were entered. No statistical analysis has been attempted.")))
                 stats_script_text = """$(function() { $("#stats_tabs0").tabs(); $("#stats_tabs1").tabs(); $("#stats_tabs2").tabs();});"""
             else:
-                #stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs")
                 stats_script_text = """$(function() { $("#stats_tabs0").tabs(); $("#stats_tabs1").tabs(); $("#stats_tabs2").tabs();});"""
             if len(vals) > 4:
                 stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-5", Class="stats_tab"),
                                                   HT.Href(text="Bar Graph (by name)", url="#statstabs-3", Class="stats_tab"), HT.Href(text="Bar Graph (by rank)", url="#statstabs-4", Class="stats_tab"),
                                                   HT.Href(text="Box Plot", url="#statstabs-2", Class="stats_tab")]
-                #stats_tabs = HT.List(stats_tab_list)
-                #stats_container.append(stats_tabs)
-                #
-                #table_div = HT.Div(id="statstabs-1")
-                #table_container = HT.Paragraph()
-                #
-                #statsTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
 
                 if this_trait.db:
                     if this_trait.cellid:
@@ -980,16 +967,6 @@ class ShowTrait(templatePage):
                 else:
                     self.stats_data.append(BasicStatisticsFunctions.basicStatsTable(vals=vals))
 
-                #statsTable.append(HT.TR(HT.TD(statsTableCell)))
-
-                #table_container.append(statsTable)
-                #table_div.append(table_container)
-                #stats_container.append(table_div)
-                #
-                #normalplot_div = HT.Div(id="statstabs-5")
-                #normalplot_container = HT.Paragraph()
-                #normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
-
                 try:
                     plotTitle = this_trait.symbol
                     plotTitle += ": "
@@ -1006,7 +983,7 @@ class ShowTrait(templatePage):
                     #normalplot_container.append(normalplot)
                     #normalplot_div.append(normalplot_container)
                     #stats_container.append(normalplot_div)
-    
+
                     #boxplot_div = HT.Div(id="statstabs-2")
                     #boxplot_container = HT.Paragraph()
                     #boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
@@ -1015,8 +992,8 @@ class ShowTrait(templatePage):
                     #boxplot_container.append(boxplot)
                     #boxplot_div.append(boxplot_container)
                     #stats_container.append(boxplot_div)
-    
-    
+
+
                     #barName_div = HT.Div(id="statstabs-3")
                     #barName_container = HT.Paragraph()
                     #barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
@@ -1034,18 +1011,6 @@ class ShowTrait(templatePage):
                     #barRank_container.append(barRank)
                     #barRank_div.append(barRank_container)
                     #stats_container.append(barRank_div)
-    
-            #    stats_cell.append(stats_container)
-            #
-            #stats_script.append(stats_script_text)
-            #
-            #submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target2")
-            #stats_row.append(stats_cell)
-    
-            #submitTable.append(stats_row)
-            #submitTable.append(stats_script)
-    
-            #title2Body.append(submitTable)
 
 
     def build_correlation_tools(self, fd, this_trait):
@@ -1053,23 +1018,13 @@ class ShowTrait(templatePage):
         #species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
 
         RISetgp = fd.RISet
-        
+
         # We're checking a string here!
         assert isinstance(RISetgp, basestring), "We need a string type thing here"
         if RISetgp[:3] == 'BXD':
             RISetgp = 'BXD'
 
         if RISetgp:
-            #sample_correlation = HT.Input(type='button',name='sample_corr', value=' Compute ', Class="button sample_corr")
-            #lit_correlation = HT.Input(type='button',name='lit_corr', value=' Compute ', Class="button lit_corr")
-            #tissue_correlation = HT.Input(type='button',name='tiss_corr', value=' Compute ', Class="button tiss_corr")
-            #methodText = HT.Span("Calculate:", Class="ffl fwb fs12")
-            #
-            #databaseText = HT.Span("Database:", Class="ffl fwb fs12")
-            #databaseMenu1 = HT.Select(name='database1')
-            #databaseMenu2 = HT.Select(name='database2')
-            #databaseMenu3 = HT.Select(name='database3')
-
             dataset_menu = []
             print("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
             print("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
@@ -1093,164 +1048,24 @@ class ShowTrait(templatePage):
             self.cursor.execute('SELECT Id, Name FROM Tissue order by Name')
             for item in self.cursor.fetchall():
                 tissue_id, tissue_name = item
-                #databaseMenuSub = HT.Optgroup(label = '%s ------' % tissue_name)
-                #dataset_sub_menu = []
-                print("phun9")
                 self.cursor.execute('''SELECT ProbeSetFreeze.FullName,ProbeSetFreeze.Name FROM ProbeSetFreeze, ProbeFreeze,
                 InbredSet WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = %s and
                 ProbeSetFreeze.public > %s and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name like %s
                 order by ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId ''',
                 (tissue_id, webqtlConfig.PUBLICTHRESH, "%" + RISetgp + "%"))
-                print("phun8")
                 dataset_sub_menu = [item for item in self.cursor.fetchall() if item]
-                #for item2 in self.cursor.fetchall():
-                #    dataset_sub_menu.append(item2)
                 if dataset_sub_menu:
                     dataset_menu.append(dict(tissue=tissue_name,
                                         datasets=dataset_sub_menu))
-                    #    ("**heading**", tissue_name))
-                    #dataset_menu.append(dataset_sub_menu)
-            
+
             dataset_menu_selected = None
             if len(dataset_menu):
                 if this_trait and this_trait.db:
                     dataset_menu_selected = this_trait.db.name
 
-                #criteriaText = HT.Span("Return:", Class="ffl fwb fs12")
-
-                #criteriaMenu1 = HT.Select(name='criteria1', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);")
-                
                 return_results_menu = (100, 200, 500, 1000, 2000, 5000, 10000, 15000, 20000)
                 return_results_menu_selected = 500
-                
-                #criteriaMenu1.append(('top 100','100'))
-                #criteriaMenu1.append(('top 200','200'))
-                #criteriaMenu1.append(('top 500','500'))
-                #criteriaMenu1.append(('top 1000','1000'))
-                #criteriaMenu1.append(('top 2000','2000'))
-                #criteriaMenu1.append(('top 5000','5000'))
-                #criteriaMenu1.append(('top 10000','10000'))
-                #criteriaMenu1.append(('top 15000','15000'))
-                #criteriaMenu1.append(('top 20000','20000'))
-
-                #self.MDPRow1 = HT.TR(Class='mdp1')
-                #self.MDPRow2 = HT.TR(Class='mdp2')
-                #self.MDPRow3 = HT.TR(Class='mdp3')
-
-            #    correlationMenus1 = HT.TableLite(
-            #            HT.TR(HT.TD(databaseText), HT.TD(databaseMenu1, colspan="3")),
-            #            HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu1)),
-            #        self.MDPRow1, cellspacing=0, width="619px", cellpadding=2)
-            #    correlationMenus1.append(HT.Input(name='orderBy', value='2', type='hidden'))    # to replace the orderBy menu
-            #    correlationMenus2 = HT.TableLite(
-            #            HT.TR(HT.TD(databaseText), HT.TD(databaseMenu2, colspan="3")),
-            #            HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu2)),
-            #        self.MDPRow2, cellspacing=0, width="619px", cellpadding=2)
-            #    correlationMenus2.append(HT.Input(name='orderBy', value='2', type='hidden'))
-            #    correlationMenus3 = HT.TableLite(
-            #            HT.TR(HT.TD(databaseText), HT.TD(databaseMenu3, colspan="3")),
-            #            HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu3)),
-            #        self.MDPRow3, cellspacing=0, width="619px", cellpadding=2)
-            #    correlationMenus3.append(HT.Input(name='orderBy', value='2', type='hidden'))
-            #
-            #else:
-            #    correlationMenus = ""
-
 
-        #corr_row = HT.TR()
-        #corr_container = HT.Div(id="corr_tabs", Class="ui-tabs")
-        #
-        #if (this_trait.db != None and this_trait.db.type =='ProbeSet'):
-        #    corr_tab_list = [HT.Href(text='Sample r', url="#corrtabs-1"),
-        #                     HT.Href(text='Literature r',  url="#corrtabs-2"),
-        #                     HT.Href(text='Tissue r', url="#corrtabs-3")]
-        #else:
-        #    corr_tab_list = [HT.Href(text='Sample r', url="#corrtabs-1")]
-        #
-        #corr_tabs = HT.List(corr_tab_list)
-        #corr_container.append(corr_tabs)
-
-        #if correlationMenus1 or correlationMenus2 or correlationMenus3:
-            #sample_div = HT.Div(id="corrtabs-1")
-            #sample_container = HT.Span()
-            #
-            #sample_type = HT.Input(type="radio", name="sample_method", value="1", checked="checked")
-            #sample_type2 = HT.Input(type="radio", name="sample_method", value="2")
-            #
-            #sampleTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
-            #sampleTD = HT.TD(correlationMenus1, HT.BR(),
-            #                           "Pearson", sample_type, "&nbsp;"*3, "Spearman Rank", sample_type2, HT.BR(), HT.BR(),
-            #                           sample_correlation, HT.BR(), HT.BR())
-            #
-            #sampleTD.append(HT.Span("The ",
-            #                        HT.Href(url="/correlationAnnotation.html#sample_r", target="_blank",
-            #                                text="Sample Correlation")," is computed between trait data and",
-            #                            " any ",HT.BR()," other traits in the sample database selected above. Use ",
-            #                            HT.Href(url="/glossary.html#Correlations", target="_blank", text="Spearman Rank"),
-            #                            HT.BR(),"when the sample size is small (<20) or when there are influential \
-            #                            outliers.", HT.BR(),Class="fs12"))
-
-            #sampleTable.append(sampleTD)
-
-            #sample_container.append(sampleTable)
-            #sample_div.append(sample_container)
-            #corr_container.append(sample_div)
-            #
-            #literature_div = HT.Div(id="corrtabs-2")
-            #literature_container = HT.Span()
-
-            #literatureTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
-            #literatureTD = HT.TD(correlationMenus2,HT.BR(),lit_correlation, HT.BR(), HT.BR())
-            #literatureTD.append(HT.Span("The ", HT.Href(url="/correlationAnnotation.html", target="_blank",text="Literature Correlation"), " (Lit r) between this gene and all other genes is computed",HT.BR(),
-            #                            "using the ", HT.Href(url="https://grits.eecs.utk.edu/sgo/sgo.html", target="_blank", text="Semantic Gene Organizer"),
-            #                            " and human, rat, and mouse data from PubMed. ", HT.BR(),"Values are ranked by Lit r, \
-            #                            but Sample r and Tissue r are also displayed.", HT.BR(), HT.BR(),
-            #                            HT.Href(url="/glossary.html#Literature", target="_blank", text="More on using Lit r"), Class="fs12"))
-            #literatureTable.append(literatureTD)
-            #
-            #literature_container.append(literatureTable)
-            #literature_div.append(literature_container)
-            #
-            #if this_trait.db != None:
-            #    if (this_trait.db.type =='ProbeSet'):
-            #        corr_container.append(literature_div)
-            #
-            #tissue_div = HT.Div(id="corrtabs-3")
-            #tissue_container = HT.Span()
-            #
-            #tissue_type = HT.Input(type="radio", name="tissue_method", value="4", checked="checked")
-            #tissue_type2 = HT.Input(type="radio", name="tissue_method", value="5")
-            #
-            #tissueTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
-            #tissueTD = HT.TD(correlationMenus3,HT.BR(),
-            #                           "Pearson", tissue_type, "&nbsp;"*3, "Spearman Rank", tissue_type2, HT.BR(), HT.BR(),
-            #                           tissue_correlation, HT.BR(), HT.BR())
-            #tissueTD.append(HT.Span("The ", HT.Href(url="/webqtl/main.py?FormID=tissueCorrelation", target="_blank", text="Tissue Correlation"),
-            #" (Tissue r) estimates the similarity of expression of two genes",HT.BR()," or \
-            #transcripts across different cells, tissues, or organs (",HT.Href(url="/correlationAnnotation.html#tissue_r", target="_blank", text="glossary"),"). \
-            #Tissue correlations",HT.BR()," are generated by analyzing expression in multiple samples usually taken from \
-            #single cases.",HT.BR(),HT.Bold("Pearson")," and ",HT.Bold("Spearman Rank")," correlations have been computed for all pairs \
-            #of genes",HT.BR()," using data from mouse samples.",
-            #HT.BR(), Class="fs12"))
-            #tissueTable.append(tissueTD)
-            #
-            #tissue_container.append(tissueTable)
-            #tissue_div.append(tissue_container)
-            #if this_trait.db != None:
-            #    if (this_trait.db.type =='ProbeSet'):
-            #        corr_container.append(tissue_div)
-            #
-            #corr_row.append(HT.TD(corr_container))
-            #
-            #corr_script = HT.Script(language="Javascript")
-            #corr_script_text = """$(function() { $("#corr_tabs").tabs(); });"""
-            #corr_script.append(corr_script_text)
-            #
-            #submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target4")
-            #submitTable.append(corr_row)
-            #submitTable.append(corr_script)
-            #
-            #title3Body.append(submitTable)
             self.corr_tools = dict(dataset_menu = dataset_menu,
                                           dataset_menu_selected = dataset_menu_selected,
                                           return_results_menu = return_results_menu,
@@ -1529,7 +1344,7 @@ class ShowTrait(templatePage):
                                         this_trait=this_trait,
                                         sample_group_type='primary',
                                         header="%s Only" % (fd.RISet))
-        
+
         print("primary_samples.attributes:", pf(primary_samples.attributes))
 
         other_sample_names = []
@@ -1553,7 +1368,7 @@ class ShowTrait(templatePage):
                                             this_trait=this_trait,
                                             sample_group_type='other',
                                             header="Non-%s" % (fd.RISet))
-            
+
             self.sample_groups = (primary_samples, other_samples)
         else:
             self.sample_groups = (primary_samples,)
@@ -1561,5 +1376,4 @@ class ShowTrait(templatePage):
         #TODO: Figure out why this if statement is written this way - Zach
         #if (other_sample_names or (fd.f1list and this_trait.data.has_key(fd.f1list[0])) 
         #        or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))):
-        #    print("hjs")
         fd.allsamplelist = all_samples_ordered
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index b89e15ce..285d5ef4 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -246,6 +246,43 @@ $ ->
     $('#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()
+    
+    show_no_value = ->
+        $('.value_se').each (index, element) =>
+            if $(element).find('.trait_value_input').val() == 'x'
+                $(element).show()
+                
+    $('#show_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) =>
+            console.log("value is:", $(element).val())
+            $(element).val($(element).data('value'))
+            console.log("data-value is:", $(element).data('value'))
+            $(element).parents('.value_se').show()
+
+    $('#reset').click(reset_samples_table)
+
+    ##End Reset Table Values Code
 
     console.log("before registering show_hide_outliers")
     $('#show_hide_outliers').click(show_hide_outliers)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 6d3dee13..d52b2756 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -11,7 +11,7 @@
   };
 
   $(function() {
-    var block_by_attribute_value, block_by_index, change_stats_value, create_value_dropdown, edit_data_change, hide_tabs, make_table, on_corr_method_change, populate_sample_attributes_values_dropdown, process_id, show_hide_outliers, stats_mdp_change, update_stat_values;
+    var block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, hide_no_value, hide_tabs, make_table, on_corr_method_change, populate_sample_attributes_values_dropdown, process_id, reset_samples_table, show_hide_outliers, show_no_value, stats_mdp_change, update_stat_values;
     hide_tabs = function(start) {
       var x, _i, _results;
       _results = [];
@@ -289,6 +289,40 @@
       }
     });
     $('#block_by_index').click(block_by_index);
+    hide_no_value = function() {
+      var _this = this;
+      return $('.value_se').each(function(index, element) {
+        if ($(element).find('.trait_value_input').val() === 'x') {
+          return $(element).hide();
+        }
+      });
+    };
+    show_no_value = function() {
+      var _this = this;
+      return $('.value_se').each(function(index, element) {
+        if ($(element).find('.trait_value_input').val() === 'x') {
+          return $(element).show();
+        }
+      });
+    };
+    $('#show_hide_no_value').click(hide_no_value);
+    block_outliers = function() {
+      var _this = this;
+      return $('.outlier').each(function(index, element) {
+        return $(element).find('.trait_value_input').val('x');
+      });
+    };
+    $('#block_outliers').click(block_outliers);
+    reset_samples_table = function() {
+      var _this = this;
+      return $('.trait_value_input').each(function(index, element) {
+        console.log("value is:", $(element).val());
+        $(element).val($(element).data('value'));
+        console.log("data-value is:", $(element).data('value'));
+        return $(element).parents('.value_se').show();
+      });
+    };
+    $('#reset').click(reset_samples_table);
     console.log("before registering show_hide_outliers");
     $('#show_hide_outliers').click(show_hide_outliers);
     console.log("after registering show_hide_outliers");
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 5a364f8b..e2ee210c 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -1310,7 +1310,7 @@
 
                               {# Todo: Add IDs #}
                               <td class="std_cell column_name-Value" align="right" width="70">
-                                <input type="text" name="{{ sample.name }}"
+                                <input type="text" data-value="{{ sample.display_value }}" name="{{ sample.name }}"
                                        class="trait_value_input edit_sample_value"
                                        value="{{ sample.display_value }}" size="8" maxlength="8"
                                        style="text-align:right; background-color:#FFFFFF;">
@@ -1323,7 +1323,7 @@
 
                               {# Todo: Add IDs #}
                               <td class="std_cell column_name-SE" align="right" width="80">
-                                <input type="text" name=""{{ 'V' + sample.name}}"
+                                <input type="text" data-value="{{ sample.display_variance }}" name=""{{ 'V' + sample.name}}"
                                        class="trait_value_input edit_sample_se"
                                        value="{{ sample.display_variance }}"
                                        size="8" maxlength="8" style="text-align:right">