Add all the source codes into the github.

1 files changed, 523 insertions, 0 deletions

diff --git a/web/webqtl/submitTrait/AddUserInputToPublishPage.py b/web/webqtl/submitTrait/AddUserInputToPublishPage.py
new file mode 100755
index 00000000..f8154266
--- /dev/null
+++ b/web/webqtl/submitTrait/AddUserInputToPublishPage.py
@@ -0,0 +1,523 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+#AddUserInputToPublishPage.py
+#
+#Classes:
+#AddUserInputToPublishPage
+#-KA
+
+import string
+from htmlgen import HTMLgen2 as HT
+import os
+import time
+
+from base.webqtlTrait import webqtlTrait
+from base.webqtlDataset import webqtlDataset
+from base.templatePage import templatePage
+from base import webqtlConfig
+from utility import webqtlUtil
+
+
+#########################################
+#      AddUserInputToPublishPage
+#########################################
+
+class AddUserInputToPublishPage(templatePage):
+
+	def __init__(self, fd):
+
+		templatePage.__init__(self, fd)
+		
+		if not self.updMysql():
+			return
+		fd.incparentsf1 = 1
+		if not fd.genotype:
+			fd.readGenotype()
+			fd.strainlist = fd.f1list + fd.strainlist
+		fd.readData()
+
+		if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']:
+			pass
+		else:
+			heading = "Add to Published Database"
+			detail = ["You don't have the permission to modify this database"]
+			self.error(heading=heading,detail=detail,error="Error")
+			return
+			
+		self.cursor.execute("""
+				SelecT 
+					PublishFreeze.Name 
+				from 
+					PublishFreeze, InbredSet 
+				where 
+					PublishFreeze.InbredSetId = InbredSet.Id AND 
+					InbredSet.Name = '%s'""" % fd.RISet)
+		
+		try:
+			self.db = webqtlDataset(self.cursor.fetchone()[0], self.cursor)
+		except:
+			heading = "Add to Published Database"
+			detail = ["The published database you requested has not been established"]
+			self.error(heading=heading,detail=detail,error="Error")
+			return
+		
+		status = fd.formdata.getvalue('curStatus')
+		if status == 'insertResult':
+			newRecord = self.readForm(fd)
+			if not newRecord:
+				return
+			else:
+				self.insertResultPage(fd, newRecord)
+		elif status == 'insertCheck':
+			newRecord = self.readForm(fd)
+			if not newRecord:
+				return
+			else:
+				self.insertCheckPage(fd, newRecord)
+		else:
+			self.dispFormPage(fd)
+	
+	def readForm(self, fd):
+		newRecord = {}
+		for field in self.db.disfield:
+			fieldValue = fd.formdata.getvalue(field)
+			if field == 'name' or field == 'sequence':
+				fieldValue = None
+			elif (not fieldValue) and (field == 'post_publication_description' or field == 'authors' or field == 'title' or field=='year'):
+				heading = "Add to Published Database"
+				detail = ["You did not enter information for %s." % webqtlUtil.formatField(field)]
+				self.error(heading=heading,detail=detail,error="Error")
+				return {}
+			elif fieldValue and field == 'pubmed_id':
+				try:
+					fieldValue = int(fieldValue)
+				except:
+					fieldValue = None
+			else:
+				pass
+			newRecord[field] = fieldValue
+		return newRecord
+		
+	def insertResultPage(self, fd, newRecord):
+		#generate html
+		if 1:
+
+			#XZ: Create new publication record if necessary
+			PublicationId = None
+			if newRecord['pubmed_id']:
+				self.cursor.execute('SelecT Id from Publication where PubMed_ID = %d' % newRecord['pubmed_id'])
+				results = self.cursor.fetchall()
+				if not results:
+					pass
+				else:
+					PublicationId = results[0][0]
+
+			if not PublicationId:
+				insertFields = ['Id']
+				self.cursor.execute('SelecT max(Id) from Publication')
+				maxId = self.cursor.fetchall()[0][0] + 1
+				insertValues = [maxId]
+				for field in self.db.disfield:
+					if field in ('authors', 'title', 'abstract', 'journal','volume','pages','month','year') and newRecord[field]:
+						insertFields.append(field)
+						insertValues.append(newRecord[field])
+				NFields = ['%s'] * len(insertFields)
+				query = "insert into Publication (%s) Values (%s)" % (string.join(insertFields, ','), string.join(NFields, ','))
+
+				self.cursor.execute(query, tuple(insertValues))
+				PublicationId = maxId
+
+
+			#XZ: Create new phenotype
+			self.cursor.execute('SelecT max(Id) from Phenotype')
+			maxId = self.cursor.fetchall()[0][0] + 1
+			PhenotypeId = maxId
+			if not newRecord['units']:
+				newRecord['units'] = "Unknown"
+
+			insertFields = ['Id']
+			insertValues = [PhenotypeId]
+			insertFields.append( 'Post_publication_description' )
+			insertValues.append( newRecord['post_publication_description'] )
+			insertFields.append( 'Units' )
+			insertValues.append( newRecord['units'] )
+			insertFields.append( 'Post_publication_abbreviation' )
+                        insertValues.append( newRecord['post_publication_abbreviation'] )
+
+			insertFields.append( 'Submitter' )
+                        insertValues.append( self.userName )
+			insertFields.append( 'Authorized_Users' )
+			insertValues.append( self.userName )
+
+			if newRecord['pre_publication_description']:
+				insertFields.append( 'Pre_publication_description' )
+				insertValues.append( newRecord['pre_publication_description'] )
+
+			insertFields.append( 'Original_description' )
+			original_desc_string = 'Original post publication description: ' + newRecord['post_publication_description']
+			if newRecord['pre_publication_description']:
+				original_desc_string = original_desc_string + '\n\nOriginal pre publication description: ' + newRecord['pre_publication_description']
+			insertValues.append( original_desc_string )
+
+			if newRecord['pre_publication_abbreviation']:
+				insertFields.append( 'Pre_publication_abbreviation' )
+				insertValues.append( newRecord['pre_publication_abbreviation'] )
+
+			if newRecord['lab_code']:
+				insertFields.append( 'Lab_code' )
+				insertValues.append( newRecord['lab_code'] )
+
+			if newRecord['owner']:
+				insertFields.append( 'Owner' )
+				insertValues.append( newRecord['owner'] )
+
+
+			NFields = ['%s'] * len(insertFields)
+			query = "insert into Phenotype (%s) Values (%s)" % (string.join(insertFields, ','), string.join(NFields, ','))
+			self.cursor.execute(query, tuple(insertValues))
+
+			
+
+
+			#XZ: Insert data into PublishData, PublishSE and NStrain tables.
+			self.cursor.execute('SelecT max(Id) from PublishData')
+			DataId = self.cursor.fetchall()[0][0] + 1
+
+			self.db.getRISet()
+			InbredSetId = self.db.risetid
+
+			self.cursor.execute('Select SpeciesId from InbredSet where Id=%s' % InbredSetId)
+			SpeciesId = self.cursor.fetchone()[0]
+
+			StrainIds = []
+			for item in fd.strainlist:
+				self.cursor.execute('Select Id from Strain where SpeciesId=%s and Name = "%s"' % (SpeciesId, item) )
+				StrainId = self.cursor.fetchall()
+				if not StrainId:
+					raise ValueError
+				else:
+					StrainIds.append(StrainId[0][0])
+			
+			for i, strainName in enumerate(fd.strainlist):
+				if fd.allTraitData.has_key(strainName):
+					tdata = fd.allTraitData[strainName]
+					traitVal, traitVar, traitNP = tdata.val, tdata.var, tdata.N
+				else:
+					continue
+					
+				if traitVal != None:
+					#print 'insert into Data values(%d, %d, %s)' % (DataId, StrainIds[i], traitVal), "<BR>"
+					#XZ, 03/05/2009: Xiaodong changed Data to PublishData
+					self.cursor.execute('insert into PublishData values(%d, %d, %s)' % (DataId, StrainIds[i], traitVal))
+				if traitVar != None:
+					#print 'insert into SE values(%d, %d, %s)' % (DataId, StrainIds[i], traitVar), "<BR>"
+					#XZ, 03/13/2009: Xiaodong changed SE to PublishSE
+					self.cursor.execute('insert into PublishSE values(%d, %d, %s)' % (DataId, StrainIds[i], traitVar))
+				if traitNP != None:
+					#print 'insert into NStrain values(%d, %d, %s)' % (DataId, StrainIds[i], traitNP), "<BR>"
+					self.cursor.execute('insert into NStrain values(%d, %d, %d)' % (DataId, StrainIds[i], traitNP))
+
+
+			self.cursor.execute('SelecT max(Sequence) from PublishXRef where InbredSetId = %d and PhenotypeId = %d and PublicationId = %d' % (InbredSetId,PhenotypeId,PublicationId))
+			Sequence = self.cursor.fetchall()
+			if not Sequence or not Sequence[0][0]:
+				Sequence = 1
+			else:
+				Sequence = Sequence[0][0] + 1
+			
+			self.cursor.execute('SelecT max(Id) from PublishXRef where InbredSetId = %d' % InbredSetId)
+			try:
+				InsertId = self.cursor.fetchall()[0][0] + 1
+			except:
+				InsertId = 10001
+			
+			ctime = time.ctime()
+			comments = "Inserted by %s at %s\n" % (self.userName, ctime)
+			#print 'insert into PublishXRef(Id, PublicationId, InbredSetId, PhenotypeId, DataId, Sequence, comments) values(%s, %s, %s, %s, %s, %s, %s)' % (InsertId , PublicationId, InbredSetId, PhenotypeId, DataId, Sequence, comments)
+			self.cursor.execute('insert into PublishXRef(Id, PublicationId, InbredSetId, PhenotypeId, DataId, Sequence, comments) values(%s, %s, %s, %s, %s, %s, %s)', (InsertId , PublicationId, InbredSetId, PhenotypeId, DataId, Sequence, comments))
+			
+			TD_LR = HT.TD(valign="top",colspan=2,bgcolor="#ffffff", height=200)
+			form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden'))
+			hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':fd.RISet, 'incparentsf1':'on'}
+			for key in hddn.keys():
+				form.append(HT.Input(name=key, value=hddn[key], type='hidden'))
+			
+			mainTitle = HT.Paragraph("Add Trait to Published Database", Class="title")
+			
+			info = HT.Paragraph("Your Trait has been succesfully added to ", self.db.genHTML(), ".")
+			
+			thisTrait = webqtlTrait(db=self.db, cursor=self.cursor, name=InsertId)
+			thisTrait.retrieveInfo()
+			
+			tbl = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0)
+			
+			checkBox = HT.Input(type="checkbox",name="searchResult",value="%s" % thisTrait)
+			tbl.append(HT.TR(HT.TD(width=30), HT.TD(thisTrait.genHTML(dispFromDatabase=1, privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users))))
+			form.append(info, HT.P(), tbl)
+			TD_LR.append(mainTitle, HT.Blockquote(form))
+			
+			self.dict['body'] = TD_LR
+		else:
+			heading = "Add to Published Database"
+			detail = ["Error occured while adding the data."]
+			self.error(heading=heading,detail=detail,error="Error")
+			return
+	
+	def insertCheckPage(self, fd, newRecord):
+		#generate html
+		form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), name='dataInput',submit=HT.Input(type='hidden'))
+		hddn = {'database':self.db.name, 'curStatus':'insertResult', 'FormID':'dataEditing', 'submitID':'addPublish', 'RISet':fd.RISet}
+		
+		recordTable = HT.TableLite(border=0, align="left")
+		title1 = HT.Paragraph("Trait Information:", Class="subtitle")
+		title2 = HT.Paragraph("Trait Data:", Class="subtitle")
+		recordInfoContainer = HT.Div(align="left")
+		recordDataContainer = HT.Div(align="left")
+		addButton = HT.Input(type='submit',name='submit', value='Add to Publish',Class="button")
+		resetButton = HT.Input(type='reset',Class="button")
+
+		recordInfoTable = HT.TableLite(border=0, cellspacing=1, cellpadding=5, align="left")
+		for field in self.db.disfield:
+			if newRecord[field]:
+				recordInfoTable.append(HT.TR(
+					HT.TD("%s :" % webqtlUtil.formatField(field), Class="fs12 fwb ff1", valign="top",align="right"),
+					HT.TD(width=20),HT.TD(newRecord[field])))
+				hddn[field] = newRecord[field]
+
+		recordInfoContainer.append(addButton, resetButton, HT.P(), title1, HT.BR(), recordInfoTable)
+		
+		recordDataTable = HT.TableLite(border=0, width = "80%",cellspacing=3, cellpadding=2)	
+		recordDataTable.append(HT.TR(HT.TD('Strain Name',Class="fs12 ffl fwb",align="left"), 
+			HT.TD('TraitData',Class="fs12 ffl fwb",align="right"), 
+			HT.TD('SE',Class="fs12 ffl fwb",align="right"),
+			HT.TD('N Per Strain',Class="fs12 ffl fwb",align="right"),
+			HT.TD('&nbsp'*8,Class="fs12 ffl fwb",align="center"),
+			HT.TD('Strain Name',Class="fs12 ffl fwb",align="left"), 
+			HT.TD('TraitData',Class="fs12 ffl fwb",align="right"), 
+			HT.TD('SE',Class="fs12 ffl fwb",align="right"),
+			HT.TD('N Per Strain',Class="fs12 ffl fwb",align="right")))
+		
+		tempTR = HT.TR(align="Center")
+		for i, strainName in enumerate(fd.strainlist):
+			if fd.allTraitData.has_key(strainName):
+				tdata = fd.allTraitData[strainName]
+				traitVal, traitVar, traitNP = tdata.val, tdata.var, tdata.N
+			else:
+				traitVal, traitVar, traitNP = None, None, None
+			
+			if traitVal != None:	
+				traitVal = "%2.3f" % traitVal
+			else:
+				traitVal = 'x'
+			if traitVar != None:	
+				traitVar = "%2.3f" % traitVar
+			else:
+				traitVar = 'x'
+			if traitNP != None:	
+				traitNP = "%d" % traitNP
+			else:
+				traitNP = 'x'
+					
+			tempTR.append(HT.TD(HT.Paragraph(strainName),align='left'), 
+				HT.TD(traitVal,align='right'), 
+				HT.TD(traitVar,align='right'),
+				HT.TD(traitNP,align='right'),
+				HT.TD('',align='center'))
+			if i % 2:
+				recordDataTable.append(tempTR)
+				tempTR = HT.TR(align="Center")
+				
+		if (i+1) % 2:
+			tempTR.append(HT.TD(''))
+			tempTR.append(HT.TD(''))
+			recordDataTable.append(tempTR)
+
+		info = HT.Paragraph("Please review the trait information and data in the text below. Check the values for errors. If no error is found, please click the \"Add to Publish\" button to submit it.")
+		recordDataContainer.append(title2, HT.BR(), info, HT.P(), recordDataTable, HT.P(), addButton, resetButton, HT.P())
+
+		recordTable.append(HT.TR(HT.TD(recordInfoContainer)), HT.TR(HT.TD(recordDataContainer)))			
+
+		webqtlUtil.exportData(hddn, fd.allTraitData, 1)
+		for key in hddn.keys():
+			form.append(HT.Input(name=key, value=hddn[key], type='hidden'))
+
+		
+		#############################
+		TD_LR = HT.TD(valign="top",colspan=2,bgcolor="#ffffff")
+		
+		mainTitle = HT.Paragraph("Add Trait to Published Database", Class="title")
+
+		form.append(recordTable)
+		
+		TD_LR.append(mainTitle, HT.Blockquote(form))
+		
+		self.dict['body'] = TD_LR
+
+	def dispFormPage(self, fd):
+		###specical care, temporary trait data
+		fullname =  fd.formdata.getvalue('fullname')
+		if fullname:
+			thisTrait = webqtlTrait(fullname=fullname, data= fd.allTraitData, cursor=self.cursor)
+			thisTrait.retrieveInfo()
+			PhenotypeValue = thisTrait.description
+		else:
+			thisTrait = webqtlTrait(data= fd.allTraitData)
+			PhenotypeValue = thisTrait.identification
+			
+		self.dict['title'] = 'Add to Published Database'
+		
+		form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), name='dataInput',submit=HT.Input(type='hidden'))
+
+		recordTable = HT.TableLite(border=0, align="left")
+		recordInfoContainer = HT.Div(align="left")
+		recordDataContainer = HT.Div(align="left")
+		title1 = HT.Paragraph("&nbsp;Trait Information:", align="left", Class="subtitle")
+		title2 = HT.Paragraph("&nbsp;Trait Data:", align="left", Class="subtitle")
+		addButton = HT.Input(type='submit',name='submit', value='Submit Trait',Class="button")
+		resetButton = HT.Input(type='reset',Class="button")
+
+		recordInfoTable = HT.TableLite(border=0, cellspacing=1, cellpadding=5,align="left")
+		for field in self.db.disfield:
+			fieldValue = ""
+
+			if field == 'comments':
+				continue
+			elif field == 'name' or field == 'sequence' or field == 'original_description' or field == 'submitter' or field == 'authorized_users':
+				form.append(HT.Input(type="hidden",name=field,value=fieldValue))
+				continue
+			elif field == 'post_publication_description':
+				inputBox = HT.Textarea(name=field, cols=60, rows=6,text=PhenotypeValue)
+			elif field == 'abstract' or field == 'pre_publication_description' or field == 'owner':
+				inputBox = HT.Textarea(name=field, cols=60, rows=6,text=fieldValue)
+			elif field == 'post_publication_abbreviation' or field == 'pre_publication_abbreviation':
+				inputBox = HT.Input(type="text",name=field,size=60, maxlength=30,value=fieldValue)
+			else:
+				inputBox = HT.Input(type="text",name=field,size=60, maxlength=255,value=fieldValue)
+			if field in ('post_publication_description', 'authors', 'title', 'year'):
+				requiredSign = HT.Span('*', Class="cr")
+			else:
+				requiredSign = ''
+				
+			recordInfoTable.append(HT.TR(
+				HT.TD(requiredSign, "%s :" % webqtlUtil.formatField(field), Class="fs12 fwb ff1", valign="top",align="right"),
+				HT.TD(width=20),HT.TD(inputBox)))
+
+			if field == 'pubmed_id':
+				recordInfoTable.append(HT.TR(
+				HT.TD(), HT.TD(width=20), 
+				HT.TD("Do not enter PubMed_ID if this trait has not been Published.", 
+					HT.BR(), "If the PubMed_ID you entered is alreday stored in our database, ",
+					HT.BR(), "all the following fields except Post Publication Description will be ignored.",
+					HT.BR(), "Do not enter any non-digit character in this field.", Class="fs11 cr")
+				))
+			if field == 'pre_publication_description':
+				recordInfoTable.append(HT.TR(
+				HT.TD(), HT.TD(width=20),
+				HT.TD("If the PubMed ID is entered, the Post Publication Description will be shown to all",
+					HT.BR(), " users. If there is no PubMed ID, and the Pre Publication Description is entered,",
+					HT.BR(), "only you and authorized users can see the Post Publication Description.", Class="fs11 cr")
+				))
+			if field == 'owner':
+				recordInfoTable.append(HT.TR(
+				HT.TD(), HT.TD(width=20),
+				HT.TD("Please provide detailed owner contact information including full name, title,",
+                                        HT.BR(), " institution, address, email etc", Class="fs11 cr")
+				))
+
+		recordInfoTable.append(HT.TR(HT.TD(HT.Span('*', Class="cr"), " Required field", align="center", colspan=3)))
+		recordInfoContainer.append(addButton, resetButton, HT.P(), title1, HT.BR(), recordInfoTable)
+
+		recordDataTable = HT.TableLite(border=0, width = "90%",cellspacing=2, cellpadding=2)
+		recordDataTable.append(HT.TR(HT.TD('Strain Name',Class="fs12 ffl fwb",align="left"), 
+			HT.TD('Trait Data',Class="fs12 ffl fwb",align="right"), 
+			HT.TD('SE',Class="fs12 ffl fwb",align="right"),
+			HT.TD('N Per Strain',Class="fs12 ffl fwb",align="right"),
+			HT.TD('&nbsp'*8,Class="fs12 ffl fwb",align="center"),
+			HT.TD('Strain Name',Class="fs12 ffl fwb",align="left"), 
+			HT.TD('Trait Data',Class="fs12 ffl fwb",align="right"), 
+			HT.TD('SE',Class="fs12 ffl fwb",align="right"),
+			HT.TD('N Per Strain',Class="fs12 ffl fwb",align="right")))
+		
+		tempTR = HT.TR(align="right")
+		for i, strainName in enumerate(fd.strainlist):
+			if thisTrait.data.has_key(strainName):
+				tdata = thisTrait.data[strainName]
+				traitVal, traitVar, traitNP = tdata.val, tdata.var, tdata.N
+			else:
+				traitVal, traitVar, traitNP = None, None, None
+			
+			if traitVal != None:	
+				traitVal = "%2.3f" % traitVal
+			else:
+				traitVal = 'x'
+			if traitVar != None:	
+				traitVar = "%2.3f" % traitVar
+			else:
+				traitVar = 'x'
+			if traitNP != None:	
+				traitNP = "%d" % traitNP
+			else:
+				traitNP = 'x'
+
+			tempTR.append(HT.TD(HT.Paragraph(strainName), width="120px", align='left'), \
+				HT.TD(HT.Input(name=fd.strainlist[i], size=8, maxlength=8, value=traitVal, align="right"), width="100px", align='right'),
+				HT.TD(HT.Input(name='V'+fd.strainlist[i], size=8, maxlength=8, value=traitVar, align="right"), width="100px", align='right'),
+				HT.TD(HT.Input(name='N'+fd.strainlist[i], size=8, maxlength=8, value=traitNP, align="right"), width="120px", align='right'),
+				HT.TD('', align='center'))
+			if i % 2:
+				recordDataTable.append(tempTR)
+				tempTR = HT.TR(align="Center")
+		
+		if (i+1) % 2:
+			tempTR.append(HT.TD(''))
+			tempTR.append(HT.TD(''))
+			tempTR.append(HT.TD(''))
+			recordDataTable.append(tempTR)
+
+		recordDataContainer.append(title2, HT.BR(), recordDataTable, HT.P(), addButton, resetButton, HT.P())
+
+		recordTable.append(HT.TR(HT.TD(recordInfoContainer)), HT.TR(HT.TD(recordDataContainer)))
+
+		"""
+		"""
+		
+		hddn = {'database':self.db.name, 'curStatus':'insertCheck', 'FormID':'dataEditing', 'submitID':'addPublish', 'RISet':fd.RISet}
+		for key in hddn.keys():
+			form.append(HT.Input(name=key, value=hddn[key], type='hidden'))
+
+		
+		#############################
+		TD_LR = HT.TD(valign="top",colspan=2,bgcolor="#ffffff")
+		
+		mainTitle = HT.Paragraph("Add Trait to Published Database", Class="title")
+		
+		form.append(recordTable)
+		
+		TD_LR.append(mainTitle, form)
+		
+		self.dict['body'] = TD_LR
+