Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

1 files changed, 0 insertions, 150 deletions

diff --git a/web/webqtl/basicStatistics/updatedBasicStatisticsPage.py b/web/webqtl/basicStatistics/updatedBasicStatisticsPage.py
deleted file mode 100755
index ab7ed07d..00000000
--- a/web/webqtl/basicStatistics/updatedBasicStatisticsPage.py
+++ /dev/null
@@ -1,150 +0,0 @@
-from htmlgen import HTMLgen2 as HT
-
-from base.templatePage import templatePage
-from dbFunction import webqtlDatabaseFunction
-import BasicStatisticsFunctions
-
-#Window generated from the Trait Data and Analysis page (DataEditingPage.py) with updated stats figures; takes the page's values that can bed edited by the user
-class updatedBasicStatisticsPage(templatePage):
-	
-	plotMinInformative = 4
-	
-	def __init__(self, fd):	
-
-		templatePage.__init__(self, fd)
-
-		if not fd.genotype:
-			fd.readGenotype()
-			this_strainlist = fd.strainlist
-
-		if fd.allstrainlist:
-			this_strainlist = fd.allstrainlist
-			
-		fd.readData(this_strainlist)
-		
-		specialStrains = [] #This appears to be the "other/non-RISet strainlist" without parents/f1 strains; not sure what to name it
-		setStrains = []
-		for item in this_strainlist:
-			if item not in fd.strainlist and item.find('F1') < 0:
-				specialStrains.append(item)
-			else:
-				continue
-			
-		specialStrains.sort()
-		if specialStrains:
-			specialStrains = fd.f1list+fd.parlist+specialStrains			
-
-		self.dict['title'] = 'Basic Statistics'
-		TD_LR = HT.TD(valign="top",width="100%",bgcolor="#fafafa")
-
-		stats_row = HT.TR()
-		stats_cell = HT.TD()
-		stats_script = HT.Script(language="Javascript")	
-
-		#Get strain names, values, and variances
-		strain_names = fd.formdata.getvalue('strainNames').split(',')
-		strain_vals = fd.formdata.getvalue('strainVals').split(',')
-		strain_vars = fd.formdata.getvalue('strainVars').split(',')
-
-		vals = []
-		if (len(strain_names) > 0):
-			if (len(strain_names) > 3):
-				#Need to create "vals" object
-				for i in range(len(strain_names)):
-					try:
-						 this_strain_val = float(strain_vals[i])
-					except:
-						 continue
-					try:
-						 this_strain_var = float(strain_vars[i])						 
-					except:
-						 this_strain_var = None
-						
-					thisValFull = [strain_names[i], this_strain_val, this_strain_var]	
-					vals.append(thisValFull)
-	
-				stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-2", 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-5", Class="stats_tab")]
-				stats_tabs = HT.List(stats_tab_list)
-				
-				stats_container = HT.Div(id="stats_tabs", Class="ui-tabs")
-				stats_container.append(stats_tabs)
-				
-				stats_script_text = """$(function() { $("#stats_tabs").tabs();});""" #Javascript enabling tabs
-				
-				table_div = HT.Div(id="statstabs-1", style="height:320px;width:740px;overflow:scroll;")
-				table_container = HT.Paragraph()	
-			
-				statsTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
-				this_trait_type = fd.formdata.getvalue('trait_type', None)
-				this_cellid = fd.formdata.getvalue('cellid', None)
-				statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=this_trait_type, cellid=this_cellid)
-				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-2", style="height:540px;width:740px;overflow:scroll;")
-				normalplot_container = HT.Paragraph()
-				normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
-				plotTitle = fd.formdata.getvalue("normalPlotTitle","")
-				normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains)
-				normalplot.append(HT.TR(HT.TD(normalplot_img)))
-				normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \
-				normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(),
-				"More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot", 
-						target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary"))))				
-				normalplot_container.append(normalplot)
-				normalplot_div.append(normalplot_container)
-				stats_container.append(normalplot_div)
-	
-				barName_div = HT.Div(id="statstabs-3", style="height:540px;width:740px;overflow:scroll;")
-				barName_container = HT.Paragraph()
-				barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
-				barName_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="name")
-				barName.append(HT.TR(HT.TD(barName_img)))		
-				barName_container.append(barName)
-				barName_div.append(barName_container)
-				stats_container.append(barName_div)
-	
-				barRank_div = HT.Div(id="statstabs-4", style="height:540px;width:740px;overflow:scroll;")
-				barRank_container = HT.Paragraph()
-				barRank = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
-				barRank_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="rank")
-				barRank.append(HT.TR(HT.TD(barRank_img)))	
-				barRank_container.append(barRank)
-				barRank_div.append(barRank_container)
-				stats_container.append(barRank_div)		
-
-				boxplot_div = HT.Div(id="statstabs-5", style="height:540px;width:740px;overflow:scroll;")
-				boxplot_container = HT.Paragraph()
-				boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
-				boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals)
-				boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left")))		
-				boxplot_container.append(boxplot)
-				boxplot_div.append(boxplot_container)
-				stats_container.append(boxplot_div)					
-	
-				stats_cell.append(stats_container)	
-				stats_script.append(stats_script_text)
-		
-				submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
-				stats_row.append(stats_cell)
-				
-				submitTable.append(stats_row)
-				submitTable.append(stats_script)
-		
-				TD_LR.append(submitTable)
-				self.dict['body'] = str(TD_LR)						
-			else:
-					heading = "Basic Statistics"
-					detail = ['Fewer than %d case data were entered for %s data set. No statitical analysis has been attempted.' % (self.plotMinInformative, fd.RISet)]
-					self.error(heading=heading,detail=detail)
-					return
-		else:
-			heading = "Basic Statistics"
-			detail = ['Empty data set, please check your data.']
-			self.error(heading=heading,detail=detail)
-			return		
\ No newline at end of file