From d0911a04958a04042da02a334ccc528dae79cc17 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 27 Mar 2015 20:28:51 +0000 Subject: Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files' --- web/webqtl/textUI/__init__.py | 0 web/webqtl/textUI/cmdClass.py | 224 ------------------------- web/webqtl/textUI/cmdCorrelation.py | 325 ------------------------------------ web/webqtl/textUI/cmdGeno.py | 118 ------------- web/webqtl/textUI/cmdGet.py | 86 ---------- web/webqtl/textUI/cmdHelp.py | 105 ------------ web/webqtl/textUI/cmdInterval.py | 174 ------------------- web/webqtl/textUI/cmdMap.py | 144 ---------------- web/webqtl/textUI/cmdSearchGene.py | 70 -------- web/webqtl/textUI/cmdShowEditing.py | 50 ------ 10 files changed, 1296 deletions(-) delete mode 100755 web/webqtl/textUI/__init__.py delete mode 100755 web/webqtl/textUI/cmdClass.py delete mode 100755 web/webqtl/textUI/cmdCorrelation.py delete mode 100755 web/webqtl/textUI/cmdGeno.py delete mode 100755 web/webqtl/textUI/cmdGet.py delete mode 100755 web/webqtl/textUI/cmdHelp.py delete mode 100755 web/webqtl/textUI/cmdInterval.py delete mode 100755 web/webqtl/textUI/cmdMap.py delete mode 100755 web/webqtl/textUI/cmdSearchGene.py delete mode 100755 web/webqtl/textUI/cmdShowEditing.py (limited to 'web/webqtl/textUI') diff --git a/web/webqtl/textUI/__init__.py b/web/webqtl/textUI/__init__.py deleted file mode 100755 index e69de29b..00000000 diff --git a/web/webqtl/textUI/cmdClass.py b/web/webqtl/textUI/cmdClass.py deleted file mode 100755 index e394218e..00000000 --- a/web/webqtl/textUI/cmdClass.py +++ /dev/null @@ -1,224 +0,0 @@ -import string -import os -import MySQLdb - -from base import webqtlConfig - -######################################### -# Basic Class -######################################### -class cmdClass: - def __init__(self,fd): - self.contents = [] - self.accessError = 0 - self.error = 0 - self.accessCode = '###Database Code : %s%s?cmd=help' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) - self.data = fd.formdata - self.cmdID = self.data.getvalue('cmd') - self.showurl = self.data.getvalue('url') - self.cursor = None - self.user_ip = fd.remote_ip - - try: - if not self.openMysql(): - self.accessError = 1 - self.contents = ['###Error: Database is not ready'] - return - - if not self.accessCount(): - self.accessError = 1 - self.contents = ['###Error: You have reached maximum access today '] - return - self.accessRecord() - except: - self.accessError = 1 - self.contents = ['###Error: Database is not ready'] - return - - - self.probeset = self.data.getvalue('probeset') - self.database = self.data.getvalue('db') - self.probe = self.data.getvalue('probe') - - self.sourcedata = [] - - - try: - self.format = self.data.getvalue('format')[:3] - except: - self.format = 'row' - if not self.probeset or not self.database: - self.error = 1 - return - - def openMysql(self): - try: - # con = MySQLdb.Connect(db='db_webqtl', host = webqtlConfig.MYSQL_SERVER) - # Modified by Fan Zhang - con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD) - self.cursor = con.cursor() - return 1 - except: - return 0 - - #XZ, 03/23/2009: The function name is confusing. This function is to get the database type(ProbeSet, Publish, Geno) id. - def getDBId(self,code): - self.cursor.execute('SELECT DBType.Name, DBList.FreezeId from DBType, DBList WHERE DBType.Id = DBList.DBTypeId and DBList.code= "%s"' % code) - result = self.cursor.fetchall() - if not result: - return (None, None) - else: - return result[0] - - #XZ, 03/23/2009: This is to get the inbredset name. - def getRISet(self,prefix, DbId): - if prefix == 'ProbeSet': - self.cursor.execute('SELECT InbredSet.Name from InbredSet, ProbeSetFreeze, ProbeFreeze WHERE ProbeFreeze.InbredSetId = InbredSet.Id and ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId and ProbeSetFreeze.Id = %d' % DbId) - else: - self.cursor.execute('SELECT InbredSet.Name from %sFreeze, InbredSet WHERE %sFreeze.InbredSetId = InbredSet.Id and %sFreeze.Id = %d' % (prefix, prefix, prefix, DbId)) - result = self.cursor.fetchall() - if result: - if result[0][0] == "BXD300": - return "BXD" - else: - return result[0][0] - else: - return None - - def accessCount(self): - try: - user_ip = self.user_ip - query = """SELECT count(id) FROM AccessLog WHERE ip_address = %s AND UNIX_TIMESTAMP()-UNIX_TIMESTAMP(accesstime)<86400""" - self.cursor.execute(query,user_ip) - daycount = self.cursor.fetchall() - if daycount: - daycount = daycount[0][0] - if daycount > webqtlConfig.DAILYMAXIMUM: - return 0 - else: - return 1 - else: - return 1 - except: - return 0 - - def accessRecord(self): - try: - user_ip = self.user_ip - self.updMysql() - query = """INSERT INTO AccessLog(accesstime,ip_address) values(Now(),%s)""" - self.cursor.execute(query,user_ip) - self.openMysql() - except: - pass - - def __str__(self): - text = map(str,self.contents) - if self.showurl: - text.append('http://%s%s?%s' % (os.environ['HTTP_HOST'],os.environ['SCRIPT_NAME'],os.environ['QUERY_STRING'][:-8])) - text += self.sourcedata - return string.join(text,'\n') - - def write(self): - if self.cursor: - self.cursor.close() - try: - browser = os.environ['HTTP_USER_AGENT'] - return '
%s
' % str(self) - except: - return str(self) - - def write2(self): - print str(self) - - def getTraitData(self, prefix, dbId, probeset, probe = None): - headerDict = {'ProbeSet':'ProbeSetID', 'Publish':'RecordID', 'Geno':'Locus'} - if prefix == None or dbId == None: - return None, None - if probe and prefix=='ProbeSet': - #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=98332_at&db=bra08-03MAS5&probe=pm&format=col - if string.lower(probe) in ("all","mm","pm"): - query = "SELECT Probe.Name from Probe, ProbeSet WHERE Probe.ProbeSetId = ProbeSet.Id and ProbeSet.Name = '%s' order by Probe.Name" % probeset - self.cursor.execute(query) - allprobes = self.cursor.fetchall() - if not allprobes: - return None, None - - fetchprobes = [] - for item in allprobes: - if probe == 'all': - fetchprobes.append(item[0]) - else: - try: - taildigit = int(item[0][-1]) % 2 - if probe == "pm" and taildigit == 1: - fetchprobes.append(item[0]) - if probe == "mm" and taildigit == 0: - fetchprobes.append(item[0]) - except: - pass - if not fetchprobes: - return None, None - #XZ, 03/05/2009: Xiaodong changed Data to ProbeData - query = "SELECT Strain.Name, ProbeData.value, Probe.Name from ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, Strain, Probe, ProbeSet WHERE ProbeSet.Name = '%s' and Probe.ProbeSetId = ProbeSet.Id and ProbeXRef.ProbeId = Probe.Id and ProbeXRef.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Id = %d and ProbeXRef.DataId = ProbeData.Id and ProbeData.StrainId = Strain.Id and Probe.Name in (%s) order by Strain.Id, Probe.Name " % (probeset,dbId, "'" + string.join(fetchprobes, "', '") +"'") - self.cursor.execute(query) - traitdata = self.cursor.fetchall() - if not traitdata: - pass - else: - nfield = len(fetchprobes) - heads = [['ProbeSet'] + [probeset]*nfield] - heads.append(['probe'] + fetchprobes) - posdict = {} - i = 0 - for item in fetchprobes: - posdict[item] = i - i += 1 - prevStrain = '' - traitdata2 = [] - i = -1 - for item in traitdata: - if item[0] != prevStrain: - prevStrain = item[0] - i += 1 - traitdata2.append([item[0]] + [None] * nfield) - else: - pass - traitdata2[i][posdict[item[-1]]+1] = item[1] - - traitdata = traitdata2 - #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=98332_at&db=bra08-03MAS5&probe=119637&format=col - else: - heads = [('ProbeSetId', probeset), ('ProbeId',probe)] - #XZ, 03/05/2009: Xiaodong changed Data to ProbeData - query = "SELECT Strain.Name, ProbeData.value from ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, Strain, Probe, ProbeSet WHERE Probe.Name = '%s' and ProbeSet.Name = '%s' and Probe.ProbeSetId = ProbeSet.Id and ProbeXRef.ProbeId = Probe.Id and ProbeXRef.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Id = %d and ProbeXRef.DataId = ProbeData.Id and ProbeData.StrainId = Strain.Id" % (probe,probeset,dbId) - #print 'Content-type: text/html\n' - self.cursor.execute(query) - traitdata = self.cursor.fetchall() - #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=98332_at&db=bra08-03MAS5&format=col - elif prefix=='ProbeSet': #XZ: probeset data - heads = [(headerDict[prefix], probeset)] - query = "SELECT Strain.Name, %sData.value from %sData, Strain, %s, %sXRef WHERE %s.Name = '%s' and %sXRef.%sId = %s.Id and %sXRef.%sFreezeId = %d and %sXRef.DataId = %sData.Id and %sData.StrainId = Strain.Id order by Strain.Id" % (prefix, prefix, prefix, prefix, prefix, probeset,prefix, prefix, prefix, prefix, prefix, dbId, prefix, prefix, prefix) - self.cursor.execute(query) - traitdata = self.cursor.fetchall() - #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=10834&db=BXDPublish&format=col - elif prefix=='Publish': - heads = [(headerDict[prefix], probeset)] - #XZ, 03/05/2009: Xiaodong changed Data to PublishData - query = "SELECT Strain.Name, PublishData.value from PublishData, Strain, PublishXRef, PublishFreeze WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId and PublishData.Id = PublishXRef.DataId and PublishXRef.Id = %s and PublishFreeze.Id = %d and PublishData.StrainId = Strain.Id" % (probeset, dbId) - self.cursor.execute(query) - traitdata = self.cursor.fetchall() - #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=rs13475701&db=BXDGeno&format=col - else: #XZ: genotype data - heads = [(headerDict[prefix], probeset)] - RISet = self.getRISet(prefix, dbId) - self.cursor.execute("select SpeciesId from InbredSet where Name = '%s'" % RISet) - speciesId = self.cursor.fetchone()[0] - #XZ, 03/05/2009: Xiaodong changed Data to %sData - query = "SELECT Strain.Name, %sData.value from %sData, Strain, %s, %sXRef WHERE %s.SpeciesId=%s and %s.Name = '%s' and %sXRef.%sId = %s.Id and %sXRef.%sFreezeId = %d and %sXRef.DataId = %sData.Id and %sData.StrainId = Strain.Id order by Strain.Id" % (prefix, prefix, prefix, prefix, prefix, speciesId, prefix, probeset,prefix, prefix, prefix, prefix, prefix, dbId, prefix, prefix, prefix) - self.cursor.execute(query) - traitdata = self.cursor.fetchall() - if traitdata: - return traitdata, heads - else: - return None, None diff --git a/web/webqtl/textUI/cmdCorrelation.py b/web/webqtl/textUI/cmdCorrelation.py deleted file mode 100755 index 04595fc5..00000000 --- a/web/webqtl/textUI/cmdCorrelation.py +++ /dev/null @@ -1,325 +0,0 @@ -# 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 - -import os -import string -from math import * -import time - -import reaper - -from base import webqtlConfig -from utility import webqtlUtil -from cmdClass import cmdClass - - -######################################### -# Correlation Class -######################################### -class cmdCorrelation(cmdClass): - - calFunction = 'webqtlUtil.calCorrelation' - - def __init__(self,fd=None): - - cmdClass.__init__(self,fd) - - if not webqtlConfig.TEXTUI: - self.contents.append("Please send your request to http://robot.genenetwork.org") - return - - - self.example = '###Example : %s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&searchdb=BXDPublish&return=500&sort=pvalue' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID) - - if self.accessError: - return - - self.searchDB = self.data.getvalue('searchdb') - if not self.searchDB or self.error: - self.contents.append("###Error: source trait doesn't exist or no target database was given") - self.contents.append(self.example) - self.contents.append(self.accessCode) - return - - try: - self.returnNumber = int(self.data.getvalue('return')) - except: - self.returnNumber = None - - self.sort = self.data.getvalue('sort') - - prefix, dbId = self.getDBId(self.database) - if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")): - self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.") - self.contents.append(self.example) - self.contents.append(self.accessCode) - return - RISet = self.getRISet(prefix, dbId) - prefix2, dbId2 = self.getDBId(self.searchDB) - if not prefix2 or not dbId2: - self.contents.append("###Error: target database doesn't exist.") - self.contents.append(self.example) - self.contents.append(self.accessCode) - return - RISet2 = self.getRISet(prefix2, dbId2) - if RISet2 != RISet: - self.contents.append("###Error: target database has different Mouse InbredSet.") - self.contents.append(self.example) - self.contents.append(self.accessCode) - return - - traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe) - if not traitdata: - self.contents.append("###Error: source trait doesn't exist.") - self.contents.append(self.example) - self.contents.append(self.accessCode) - return - - StrainNames = [] - sourceTrait = [] - StrainIds = [] - - #XZ, Jan 27, 2011: Only the strains that are of the same inbredset are used to calculate correlation. - for item in traitdata: - one_strain_name = item[0] - one_strain_value = item[1] - - self.cursor.execute('SELECT Strain.Id from Strain,StrainXRef, InbredSet WHERE Strain.Name="%s" and Strain.Id = StrainXRef.StrainId and StrainXRef.InbredSetId = InbredSet.Id and InbredSet.Name = "%s"' % (one_strain_name, RISet2)) - Results = self.cursor.fetchall() - if Results: - StrainIds.append('%d' % Results[0][0]) - StrainNames.append( one_strain_name ) - sourceTrait.append( one_strain_value ) - - correlationArray = [] - - useFastMethod = False - if prefix2 == "ProbeSet": - DatabaseFileName = self.getFileName( target_db_id=dbId2 ) - DirectoryList = os.listdir(webqtlConfig.TEXTDIR) ### List of existing text files. Used to check if a text file already exists - if DatabaseFileName in DirectoryList: - useFastMethod = True - - if useFastMethod: - datasetFile = open(webqtlConfig.TEXTDIR+DatabaseFileName,'r') - - #XZ, 01/08/2009: read the first line - line = datasetFile.readline() - dataset_strains = webqtlUtil.readLineCSV(line)[1:] - - #XZ, 01/08/2009: This step is critical. It is necessary for this new method. - _newvals = [] - for item in dataset_strains: - if item in StrainNames: - _newvals.append(sourceTrait[StrainNames.index(item)]) - else: - _newvals.append('None') - - nnCorr = len(_newvals) - - - for line in datasetFile: - traitdata=webqtlUtil.readLineCSV(line) - traitdataName = traitdata[0] - traitvals = traitdata[1:] - - corr,nOverlap = webqtlUtil.calCorrelationText(traitvals,_newvals,nnCorr) - traitinfo = [traitdataName,corr,nOverlap] - correlationArray.append( traitinfo ) - - #calculate correlation with slow method - else: - correlationArray = self.calCorrelation(sourceTrait, self.readDB(StrainIds, prefix2, dbId2) ) - - correlationArray.sort(self.cmpCorr) #XZ: Do not forget the sort step - - if not self.returnNumber: - correlationArray = correlationArray[:100] - else: - if self.returnNumber < len(correlationArray): - correlationArray = correlationArray[:self.returnNumber] - NN = len(correlationArray) - for i in range(NN): - nOverlap = correlationArray[i][-1] - corr = correlationArray[i][-2] - if nOverlap < 3: - corrPValue = 1.0 - else: - if abs(corr) >= 1.0: - corrPValue = 0.0 - else: - ZValue = 0.5*log((1.0+corr)/(1.0-corr)) - ZValue = ZValue*sqrt(nOverlap-3) - corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue))) - correlationArray[i].append(corrPValue) - if self.sort == 'pvalue': - correlationArray.sort(self.cmpPValue) - - if prefix2 == 'Publish': - self.contents.append("RecordID\tCorrelation\t#Strains\tp-value") - elif prefix2 == 'Geno': - self.contents.append("Locus\tCorrelation\t#Strains\tp-value") - else: - pass - - if prefix2 == 'Publish' or prefix2 == 'Geno': - for item in correlationArray: - self.contents.append("%s\t%2.6f\t%d\t%2.6f" % tuple(item)) - else: - id = self.data.getvalue('id') - if id == 'yes': - self.contents.append("ProbesetID\tCorrelation\t#Strains\tp-value\tGeneID") - for item in correlationArray: - query = """SELECT GeneID from %s WHERE Name = '%s'""" % (prefix2,item[0]) - self.cursor.execute(query) - results = self.cursor.fetchall() - if not results: - item = item + [None] - else: - item = item + list(results[0]) - self.contents.append("%s\t%2.6f\t%d\t%2.6f\t%s" % tuple(item)) - elif id == 'only': - self.contents.append("GenID") - for item in correlationArray: - query = """SELECT GeneID from %s WHERE Name = '%s'""" % (prefix2,item[0]) - self.cursor.execute(query) - results = self.cursor.fetchall() - if not results: - self.contents.append('None') - else: - self.contents.append(results[0][0]) - else: - self.contents.append("ProbesetID\tCorrelation\t#Strains\tp-value") - for item in correlationArray: - self.contents.append("%s\t%2.6f\t%d\t%2.6f" % tuple(item)) - - - - - def getFileName(self, target_db_id): - - query = 'SELECT Id, FullName FROM ProbeSetFreeze WHERE Id = %s' % target_db_id - self.cursor.execute(query) - result = self.cursor.fetchone() - Id = result[0] - FullName = result[1] - FullName = FullName.replace(' ','_') - FullName = FullName.replace('/','_') - - FileName = 'ProbeSetFreezeId_' + str(Id) + '_FullName_' + FullName + '.txt' - - return FileName - - - - def calCorrelation(self,source,target): - allcorrelations = [] - NN = len(source) - - if len(source) != len(target[0]) - 1: - return allcorrelations - else: - for traitData in target: - corr,nOverlap = eval("%s(traitData[1:],source,NN)" % self.calFunction) - traitinfo = [traitData[0],corr,nOverlap] - allcorrelations.append(traitinfo) - - return allcorrelations - - def cmpCorr(self,A,B): - try: - if abs(A[1]) < abs(B[1]): - return 1 - elif abs(A[1]) == abs(B[1]): - return 0 - else: - return -1 - except: - return 0 - - def cmpPValue(self,A,B): - try: - if A[-1] > B[-1]: - return 1 - elif A[-1] == B[-1]: - return 0 - else: - return -1 - except: - return 0 - - - def readDB(self, StrainIds=[], prefix2='', dbId2=''): - - #retrieve data from target database - nnn = len(StrainIds) / 25 - if len(StrainIds) % 25: - nnn += 1 - oridata = [] - for step in range(nnn): - temp = [] - StrainIdstep = StrainIds[step*25:min(len(StrainIds), (step+1)*25)] - for item in StrainIdstep: - temp.append('T%s.value' % item) - #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=BXDPublish&return=500&sort=pvalue - if prefix2 == "Publish": - query = "SELECT PublishXRef.Id, " - dataStartPos = 1 - query += string.join(temp,', ') - query += ' from (PublishXRef, PublishFreeze)\n' - #XZ, 03/05/2009: Xiaodong changed Data to PublishData - for item in StrainIdstep: - query += 'left join PublishData as T%s on T%s.Id = PublishXRef.DataId and T%s.StrainId=%s\n' %(item,item,item,item) - query += "WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId and PublishFreeze.Id = %d" % (dbId2, ) - #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=HC_M2_1005_M&return=500&sort=pvalue - #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=BXDGeno&return=500&sort=pvalue - else: - query = "SELECT %s.Name," % prefix2 - query += string.join(temp,', ') - query += ' from (%s, %sXRef, %sFreeze) \n' % (prefix2,prefix2,prefix2) - #XZ, 03/05/2009: Xiaodong changed Data to %sData - for item in StrainIdstep: - query += 'left join %sData as T%s on T%s.Id = %sXRef.DataId and T%s.StrainId=%s\n' %(prefix2,item,item,prefix2,item,item) - query += "WHERE %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Id = %d and %s.Id = %sXRef.%sId" % (prefix2, prefix2, prefix2, prefix2, dbId2, prefix2, prefix2, prefix2) - self.cursor.execute(query) - results = self.cursor.fetchall() - if not results: - self.contents.append("###Error: target database doesn't exist.") - self.contents.append(self.example) - self.contents.append(self.accessCode) - return - oridata.append(results) - - datasize = len(oridata[0]) - targetTrait = [] - for j in range(datasize): - traitdata = list(oridata[0][j]) - for i in range(1,nnn): - traitdata += list(oridata[i][j][1:]) - targetTrait.append(traitdata) - - return targetTrait - diff --git a/web/webqtl/textUI/cmdGeno.py b/web/webqtl/textUI/cmdGeno.py deleted file mode 100755 index 8dd0f924..00000000 --- a/web/webqtl/textUI/cmdGeno.py +++ /dev/null @@ -1,118 +0,0 @@ -# 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 - -import string -import os - -import reaper - -from base import webqtlConfig -from cmdClass import cmdClass - -######################################### -# Geno Class -######################################### -class cmdGeno(cmdClass): - - def __init__(self,fd=None): - - cmdClass.__init__(self,fd) - - if not webqtlConfig.TEXTUI: - self.contents.append("Please send your request to http://robot.genenetwork.org") - return - - if self.accessError: - return - self.error = 0 - self.RISet = None - self.chr = None - self.dataset = None - self.strainList = [] - try: - self.RISet = self.data.getvalue('riset') - if not self.RISet: - raise ValueError - except: - self.error = 1 - self.contents.append('###Example : http://www.genenetwork.org%s%s?cmd=%s&riset=BXD&chr=1' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)) - return - try: - self.format = self.data.getvalue('format')[:3] - except: - self.format = 'row' - - try: - self.dataset = reaper.Dataset() - try: - self.dataset.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno')) - except: - self.dataset.read(os.path.join(webqtlConfig.GENODIR, self.RISet.upper() + '.geno')) - self.strainList = list(self.dataset.prgy) - except: - self.error = 1 - #traceback.print_exc() - self.contents.append('###The name of RISet is incorrect') - return - - try: - self.chr = self.data.getvalue('chr') - if self.chr: - if self.chr == 'X' or self.chr == 'x': - self.chr = '20' - self.chr = int(self.chr) - except: - pass - - self.readGeno() - - def readGeno(self): - try: - table = [['Chr'] + ['Locus'] + self.strainList] - if self.chr: - chr = self.dataset[self.chr-1] - for locus in chr: - items = string.split(string.join(locus.genotext, " ")) - items = [chr.name] + [locus.name] + items - table += [items] - else: - for chr in self.dataset: - for locus in chr: - items = string.split(string.join(locus.genotext, " ")) - items = [chr.name] + [locus.name] + items - table += [items] - if self.format == 'col': - table = [[r[col] for r in table] for col in range(1, len(table[0]))] - table[0][0] = 'Line' - lines = string.join(map(lambda x: string.join(x, '\t'), table), '\n') - self.contents.append(lines) - except: - self.contents =['###Error: Read file error or name of chromosome is incorrect'] - #traceback.print_exc() - return - - - diff --git a/web/webqtl/textUI/cmdGet.py b/web/webqtl/textUI/cmdGet.py deleted file mode 100755 index a11c97a3..00000000 --- a/web/webqtl/textUI/cmdGet.py +++ /dev/null @@ -1,86 +0,0 @@ -# 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 - -import string - -from base import webqtlConfig -from cmdClass import cmdClass - -######################################### -# Get trait value Class -######################################### -class cmdGet(cmdClass): - def __init__(self,fd=None): - - cmdClass.__init__(self,fd) - - if not webqtlConfig.TEXTUI: - self.contents.append("Please send your request to http://robot.genenetwork.org") - return - - self.example = '###Example : %s%s?cmd=%s&probeset=100001_at&db=bra03-03Mas5&probe=all' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID) - if self.accessError: - return - if not self.error: - self.readDB() - else: - self.contents.append(self.example) - self.contents.append(self.accessCode) - - def readDB(self): - prefix, dbId = self.getDBId(self.database) - - traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe) - try: - if not traitdata: - raise ValueError - traitdata = heads + list(traitdata) - if self.format == 'col': - self.formatCols(traitdata) - else: - self.formatRows(traitdata) - except: - self.contents.append('Error: no record was found') - self.contents.append(self.accessCode) - return - - def formatCols(self, traitdata): - for item in traitdata: - lines = [] - for item2 in item: - lines.append(item2) - lines = string.join(map(str,lines), '\t') - self.contents.append(lines) - - def formatRows(self, traitdata): - for i in range(len(traitdata[0])): - lines = [] - for j in range(len(traitdata)): - lines.append(traitdata[j][i]) - lines = string.join(map(str,lines), '\t') - self.contents.append(lines) - - diff --git a/web/webqtl/textUI/cmdHelp.py b/web/webqtl/textUI/cmdHelp.py deleted file mode 100755 index 754ff5b5..00000000 --- a/web/webqtl/textUI/cmdHelp.py +++ /dev/null @@ -1,105 +0,0 @@ -# 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 - -import string - -from base import webqtlConfig -from base.admin import ADMIN_tissue_alias -from cmdClass import cmdClass - -######################################### -# Help Class -######################################### - -#XZ, 03/23/2009: There are several issues need attention. -#1. Some probeset datasets are not added into DBList. -#2. Do NOT show confidential datasets. -#3. Get rid of ADMIN_tissue_alias. We should use info from database instead. - -class cmdHelp(cmdClass): - def __init__(self,fd=None): - - cmdClass.__init__(self,fd) - - if not webqtlConfig.TEXTUI: - self.contents.append("Please send your request to http://robot.genenetwork.org") - return - - - machineParse = self.data.getvalue('parse') - topic = self.data.getvalue('topic') - if topic: - topic = topic.lower() - if topic == 'tissue': - self.contents.append("%s%s| %s" %("Tissue", ' '*(50-len("Tissue")), "Tissue Abbreviations")) - self.contents.append("%s%s| %s" %("", ' '*50, "(Separated by space, case insensitive)")) - self.contents.append("%s|%s" %('_'*50, '_'*40)) - - keys = ADMIN_tissue_alias.keys() - keys.sort() - for key in keys: - self.contents.append("%s%s| %s" % (key , ' '*(50-len(key)), string.join(ADMIN_tissue_alias[key], " "))) - self.contents.append("%s|%s" %('_'*50, '_'*40)) - else: - pass - else: - self.contents = ["#Use database code table below to access data", "#For machine parse friendly output please use", - "#http://www.genenetwork.org%s%s?cmd=help&parse=machine" % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)] - self.cursor.execute("""(SELECT DBType.Name, DBList.FreezeId, DBList.Code, ProbeSetFreeze.CreateTime as Time - from ProbeSetFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and - DBType.Name = 'ProbeSet' and DBList.FreezeId = ProbeSetFreeze.Id and - ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime ,DBList.Name, DBList.Id) - UNION - (SELECT DBType.Name, DBList.FreezeId, DBList.Code, PublishFreeze.CreateTime as Time - from PublishFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and - DBType.Name = 'Publish' and DBList.FreezeId = PublishFreeze.Id order by - PublishFreeze.CreateTime ,DBList.Name, DBList.Id) - UNION - (SELECT DBType.Name, DBList.FreezeId, DBList.Code, GenoFreeze.CreateTime - from GenoFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and - DBType.Name = 'Geno' and DBList.FreezeId = GenoFreeze.Id order by - GenoFreeze.CreateTime ,DBList.Name, DBList.Id)""" % webqtlConfig.PUBLICTHRESH) - dbs = self.cursor.fetchall() - if machineParse =="machine": - pass - else: - self.contents.append("\n") - self.contents.append("%s%s| %s" %("Database_Name", ' '*(50-len("Database_Name")), "Database_Access_Code_Name")) - self.contents.append("%s|%s" %('_'*50, '_'*40)) - for dbInfo in dbs: - self.cursor.execute('SELECT FullName from %sFreeze WHERE Id = %d and public > %d' % (dbInfo[0], dbInfo[1],webqtlConfig.PUBLICTHRESH)) - results = self.cursor.fetchall() - if not results: - pass - else: - if machineParse =="machine": - self.contents.append(results[0][0]+ ',' +dbInfo[2]) - else: - self.contents.append("%s%s| %s" %(results[0][0], ' '*(50-len(results[0][0])), dbInfo[2])) - self.contents.append("%s|%s" %('_'*50, '_'*40)) - - - diff --git a/web/webqtl/textUI/cmdInterval.py b/web/webqtl/textUI/cmdInterval.py deleted file mode 100755 index 0b97c7c3..00000000 --- a/web/webqtl/textUI/cmdInterval.py +++ /dev/null @@ -1,174 +0,0 @@ -# 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 - -import string -import os - -import reaper - -from base import webqtlConfig -from cmdClass import cmdClass - -######################################### -# Interval Mapping Class -######################################### -class cmdInterval(cmdClass): - - def __init__(self,fd=None): - - cmdClass.__init__(self,fd) - - if not webqtlConfig.TEXTUI: - self.contents.append("Please send your request to http://robot.genenetwork.org") - return - - - self.example = '###Example : %s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=pos&return=100&chr=12' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID) - if self.accessError: - return - self.sort = None - self.step = 0.01 - self.peak = 1 - self.chr = None - self.sort = None - self.returnnumber = 20 - if self.error: - self.error = 1 - self.contents.append(self.example) - return - else: - try: - self.sort = self.data.getvalue('sort') - if string.lower(self.sort) == 'pos': - self.sort = 'pos' - else: - self.sort = 'lrs' - except: - self.sort = None - - try: - self.returnnumber = int(self.data.getvalue('return')) - except: - self.returnnumber = 20 - try: - self.chr = self.data.getvalue('chr') - except: - self.chr = None - - self.readDB() - - def readDB(self): - prefix, dbId = self.getDBId(self.database) - if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")): - self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.") - self.contents.append(self.example) - self.contents.append(self.accessCode) - return - RISet = self.getRISet(prefix, dbId) - traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe) - if not traitdata: - self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.") - self.contents.append(self.example) - self.contents.append(self.accessCode) - return - - dataset0 = reaper.Dataset() - dataset0.read(os.path.join(webqtlConfig.GENODIR, RISet + '.geno')) - strainList = list(dataset0.prgy) - dataset = dataset0.addinterval() - if self.chr != None: - for _chr in dataset: - if string.lower(_chr.name) == string.lower(self.chr): - dataset.chromosome = [_chr] - break - - strains = [] - trait = [] - _prgy = dataset.prgy - for item in traitdata: - if item[0] in _prgy: - strains.append(item[0]) - trait.append(item[1]) - - qtlscan = dataset.regression(strains, trait) - LRS = dataset.permutation(strains, trait) - nperm = len(LRS) - - #print inter1[0] - returnPeak = [] - nqtl = len(qtlscan) - if self.peak: - for i in range(nqtl): - if i == 0 or qtlscan[i].locus.chr != qtlscan[i-1].locus.chr: - if qtlscan[i].lrs < qtlscan[i+1].lrs: - continue - elif i == nqtl-1 or qtlscan[i].locus.chr != qtlscan[i+1].locus.chr: - if qtlscan[i].lrs < qtlscan[i-1].lrs: - continue - else: - if qtlscan[i].lrs < qtlscan[i+1].lrs or qtlscan[i].lrs < qtlscan[i-1].lrs: - continue - returnPeak.append(qtlscan[i]) - else: - returnPeak = qtlscan[:] - - if returnPeak: - self.contents.append("Locus\tLRS\tChr\tAdditive\tp-value\tcM") - qtlresult = [] - for item in returnPeak: - p_value = reaper.pvalue(item.lrs,LRS) - qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value, item.locus.cM)) - if self.sort == 'lrs': - qtlresult.sort(self.cmpLRS2) - for item in qtlresult: - self.contents.append("%s\t%2.4f\t%s\t%2.4f\t%1.4f\t%s" % item) - else: - self.contents.append("###Error: Error occurs while regression.") - return - - def cmpPValue(self,A,B): - try: - if A[-1] > B[-1]: - return 1 - elif A[-1] == B[-1]: - return 0 - else: - return -1 - except: - return 0 - - def cmpLRS2(self,A,B): - try: - if A[1] < B[1]: - return 1 - elif A[1] == B[1]: - return 0 - else: - return -1 - except: - return 0 - - diff --git a/web/webqtl/textUI/cmdMap.py b/web/webqtl/textUI/cmdMap.py deleted file mode 100755 index 1fbff5a5..00000000 --- a/web/webqtl/textUI/cmdMap.py +++ /dev/null @@ -1,144 +0,0 @@ -# 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 - -import string -import os - -import reaper - -from base import webqtlConfig -from cmdClass import cmdClass - - -######################################### -# Mapping Class -######################################### -class cmdMap(cmdClass): - - def __init__(self,fd=None): - - cmdClass.__init__(self,fd) - - if not webqtlConfig.TEXTUI: - self.contents.append("Please send your request to http://robot.genenetwork.org") - return - - self.example = '###Example : %s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=lrs&return=20' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID) - if self.accessError: - return - try: - self.returnnumber = int(self.data.getvalue('return')) - except: - self.returnnumber = None - - if self.error: - self.contents.append(self.example) - self.contents.append(self.accessCode) - else: - self.sort = self.data.getvalue('sort') - self.readDB() - - def readDB(self): - prefix, dbId = self.getDBId(self.database) - if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")): - self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.") - self.contents.append(self.example) - self.contents.append(self.accessCode) - return - RISet = self.getRISet(prefix, dbId) - traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe) - if not traitdata: - self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.") - self.contents.append(self.example) - self.contents.append(self.accessCode) - return - - dataset = reaper.Dataset() - dataset.read(os.path.join(webqtlConfig.GENODIR, RISet + '.geno')) - strainList = list(dataset.prgy) - - strains = [] - trait = [] - _prgy = dataset.prgy - for item in traitdata: - if item[0] in _prgy: - strains.append(item[0]) - trait.append(item[1]) - - qtlscan = dataset.regression(strains, trait) - LRS = dataset.permutation(strains, trait) - nperm = len(LRS) - if qtlscan: - self.contents.append("Locus\tLRS\tChr\tAdditive\tp-value") - qtlresult = [] - if self.returnnumber: - self.returnnumber = min(self.returnnumber,len(qtlscan)) - if self.sort == 'lrs': - qtlscan.sort(self.cmpLRS) - for item in qtlscan[:self.returnnumber]: - p_value = reaper.pvalue(item.lrs,LRS) - qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value)) - else:#sort by position - qtlscan2 = qtlscan[:] - qtlscan2.sort(self.cmpLRS) - LRSthresh = qtlscan2[self.returnnumber].lrs - for item in qtlscan: - if item.lrs >= LRSthresh: - p_value = reaper.pvalue(item.lrs,LRS) - qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value)) - else: - for item in qtlscan: - p_value = reaper.pvalue(item.lrs,LRS) - qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value)) - if self.sort == 'lrs': - qtlresult.sort(self.cmpLRS2) - for item in qtlresult: - self.contents.append("%s\t%2.5f\t%s\t%2.5f\t%1.5f" % item) - else: - self.contents.append("###Error: Error occurs while regression.") - return - - def cmpLRS(self,A,B): - try: - if A.lrs < B.lrs: - return 1 - elif A.lrs == B.lrs: - return 0 - else: - return -1 - except: - return 0 - - def cmpLRS2(self,A,B): - try: - if A[1] < B[1]: - return 1 - elif A[1] == B[1]: - return 0 - else: - return -1 - except: - return 0 diff --git a/web/webqtl/textUI/cmdSearchGene.py b/web/webqtl/textUI/cmdSearchGene.py deleted file mode 100755 index c2c71815..00000000 --- a/web/webqtl/textUI/cmdSearchGene.py +++ /dev/null @@ -1,70 +0,0 @@ -# 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 - -import string - -from cmdClass import cmdClass -from search.TextSearchPage import TextSearchPage - -######################################### -# Search Gene Symbol PAGE -######################################### -class cmdSearchGene(cmdClass): - def __init__(self,fd): - #example - cmdClass.__init__(self,fd) - self.page = None - self.text = "" - fd.geneName = fd.formdata.getvalue('gene') - fd.returnFmt = fd.formdata.getvalue('format', 'html') - if fd.geneName: - fd.geneName = string.strip(fd.geneName) - fd.refseq = fd.formdata.getvalue('refseq') - if fd.refseq: - fd.refseq = string.strip(fd.refseq) - fd.genbankid = fd.formdata.getvalue('genbankid') - if fd.genbankid: - fd.genbankid = string.strip(fd.genbankid) - fd.geneid = fd.formdata.getvalue('geneid') - if fd.geneid: - fd.geneid = string.strip(fd.geneid) - if 1: - if not (fd.geneName or fd.refseq or fd.genbankid or fd.geneid): - raise "ValueError" - fd.searchAlias = fd.formdata.getvalue('alias') - if fd.searchAlias != '1': - fd.searchAlias = None - self.page = TextSearchPage(fd) - if fd.returnFmt != 'text': - pass - else: - self.text = self.page.output - self.page = None - elif "ValueError": - self.text = "You need to submit a Gene name, a Refseq ID, or a GenBank ID" - else: - self.text = "Error occurs while searching the database" - diff --git a/web/webqtl/textUI/cmdShowEditing.py b/web/webqtl/textUI/cmdShowEditing.py deleted file mode 100755 index 918e83a7..00000000 --- a/web/webqtl/textUI/cmdShowEditing.py +++ /dev/null @@ -1,50 +0,0 @@ -# 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 - -from cmdClass import cmdClass -from showTrait.ShowTraitPage import ShowTraitPage - - -######################################### -# SHOW DATA-EDITING PAGE -######################################### -class cmdShowEditing(cmdClass): - def __init__(self,fd): - ###example = http://www.webqtl.org/cgi-bin/beta/WebQTL?cmd=snp&chr=1&start=0&end=21345677 - cmdClass.__init__(self,fd) - self.page = None - prefix, dbId = self.getDBId(self.database) - try: - if not prefix or not dbId: - raise ValueError - self.cursor.execute('SELECT Name from %sFreeze WHERE Id=%d' % (prefix, dbId)) - database = self.cursor.fetchall()[0][0] - traitInfos = (database,self.probeset,self.probe) - self.page = ShowTraitPage(fd,traitInfos) - #self = page - except: - print "Database Name Incorrect" - -- cgit v1.2.3