def sendmailPB(s,projName,projpp,EMailAdd,goodbyeText):
# this function is for shared and private project Information and Project established notice.
import os, smtplib
import time
from userName import userName
if userName()[1]!='' or userName()[2]!='':
FLName=userName()[1]+' '+userName()[2]
else:
FLName=os.environ['LOGNAME']
From=EMailAdd
To=EMailAdd
Date = time.ctime(time.time())
Subject = "Project initialization: \'%s\'" %(projName)
Text = '''\n%s\nTo unjoin the project, please login analysis.xxx.xxx.xxx, copy and paste the following line at your shell's prompt:
unjoin.project %s\n
Let us cooperate to get this project well done.\n
Sincerely,
%s
Email: %s
''' %(goodbyeText,projpp, FLName,From) #os.environ['LOGNAME']
#Format mail message
mMessage = ('From: %s\nTo: %s\nDate: %s\nSubject: %s\n%s\n' %
(From, To, Date, Subject, Text))
rCode = s.sendmail(From, To, mMessage)
s.quit()
if rCode:
print 'Error Sending Message. Please verify your emaill address.'
def sendmailSI(s,projName,projpp,EMailAdd):
# this function is for shared project Invitation
import os, smtplib
import time
from userName import userName
if userName()[1]!='' or userName()[2]!='':
FLName=userName()[1]+' '+userName()[2]
else:
FLName=os.environ['LOGNAME']
From=EMailAdd
To=EMailAdd
Date = time.ctime(time.time())
Subject = "Project Invitation: \'%s\'" %(projName)
Text = '''Dear project analyst:\n
You are invited to join the project: %s.\n
Instructions to join:
1. login analysis.xxx.xxx.xxx using your Unix user id and password.
2. run the following command at the command line
join.project %s\n
Instructions to unjoin:
1. login analysis.xxx.xxx.xxx using your Unix user id and password.
2. run the following command at the command line
unjoin.project %s\n
Let us cooperate to get this project well done.\n
Sincerely,
%s
Email: %s
''' %(projName, projpp, projpp, FLName,From)
#Format mail message
mMessage = ('From: %s\nTo: %s\nDate: %s\nSubject: %s\n%s\n' %
(From, To, Date, Subject, Text))
rCode = s.sendmail(From, To, mMessage)
s.quit()
if rCode:
print 'Error Sending Message. Please verify your email address.'
else:
print '\nTwo auto generated emails have been successfully sent to you at %s.' %(To)
print 'To invite other project member(s), please forward the Project Invitation Email.\n'
def _inputAnalyst(self):
if self.pattern=='verbose':
moreAnalyst = 1
while moreAnalyst >0:
analyst = {}
cask=0
while cask==0:
try:
AnaNameQ="Your FirstName and LastName: [%s %s] " %(userName()[1],userName()[2])
RAnaNameQ=raw_input(AnaNameQ)
if RAnaNameQ!='' and RAnaNameQ!='\n':
analystFname,analystLname = RAnaNameQ.split()
analystLname = analystLname.strip()
else:
analystFname=userName()[1]
analystLname=userName()[2]
cask=1
except:
print "Please input the information in the formate as in the [ ]"
analystType = raw_input("Category (1: Ph.D statistician, 2: MS statistician, 3: Stats Programmer): ")
while analystType not in ('1','2','3'):
analystType = raw_input("Only 1, 2 or 3 are valid: ")
analyst['firstName'] = analystFname
analyst['lastName'] = analystLname
analyst['category'] = analystType
analyst['email'] = 'NoValue'
analyst['joinDate'] = time.ctime()
analyst['unjoinDate'] ='NoValue' #time.asctime(time.strptime("1 Jan 00 1:1am", "%d %b %y %I:%M%p")) #'Sat Jan 1 01:01:00 2000'
analyst['loginName']=os.environ['USER']
self.analysts.append(analyst)
moreAnalyst = -1
if self.pattern=='non-verbose':
analyst = {}
if userName()[1]!='':
analyst['firstName'] = userName()[1]
else:
analyst['firstName'] =' '
if userName()[2]!='':
analyst['lastName'] = userName()[2]
else:
analyst['lastName'] =' '
analyst['category'] = ' '
analyst['email'] = 'NoValue'
analyst['joinDate'] = time.ctime()
analyst['unjoinDate'] ='NoValue' #time.asctime(time.strptime("1 Jan 00 1:1am", "%d %b %y %I:%M%p")) #'Sat Jan 1 01:01:00 2000'
analyst['loginName']=os.environ['USER']
self.analysts.append(analyst)
def wipeProj(projPathAtRemote):
import os, sys, pwd, stat
from xml.dom import minidom
from osWalk import walktree
from userName import userName
from UnjoinMail import UnjoinMailSub
from pathInfo import pathInfo_j
from unjoinProj import unjoinProj
from snipTree import snipTree
projPathInfo = pathInfo_j(projPathAtRemote)
# pathInfo: pathOutput=(pathAbs,projName,projNameA,projNameP,projNameAP,pathPrefix,secId,pidType)
# 0 1 2 3 4 5 6 7
#
secId = projPathInfo[6]
pidType = projPathInfo[7]
projName = projPathInfo[1]
# give project path (with proj name), relative to pathPrefix as in pathInfo.py
projNameP = projPathInfo[3]
pathPrefix = projPathInfo[5]
if pidType == "private":
pid = 1
elif pidType == "shared":
pid = 3
else:
sys.exit("Wrong project type, contact support")
if secId == "BIOSTAT":
secIdN = 1
elif secId == "BIOINFO":
secIdN = 2
else:
sys.exit("Wrong section ID, contact support")
print "\nYou are going to permanently wipe out a project with the following parameters:"
print " Section : %s" % (projPathInfo[6])
print " Project Type : %s" % (projPathInfo[7])
print " Local Project Path : %s" % (projPathInfo[9])
print "Remote Project Path : %s\n" % (projPathInfo[0])
pathVerify = raw_input("Is the above information correct [y] (y/n) ? ")
pathVerify = pathVerify.upper()
while not (pathVerify in ["", "Y", "N", "YES", "NO"]):
print 'Please answer with "y" or "n" '
pathVerify = raw_input("Are these correct [y] (y/n)? ")
pathVerify = pathVerify.upper()
if pathVerify in ["N", "NO"]:
sys.exit("\n")
# #########################################
projPathAtRemote = projPathInfo[0] # os.path.abspath(projPathAtRemote)
ProjToBeUnjoind = projPathInfo[1] # projPathAtRemote.split('/')[-1]
# name of the project to be unjoined
# #########################################
while not os.path.exists(projPathAtRemote):
print "\nThere is no project as your input ('%s'). \nPlease verify the project name and directory path.\n" % (
projPathAtRemote
)
continueDel = raw_input("Do you wan to specify another project to wipe out? y/n: ")
print "\n"
if continueDel.strip().upper() == "N":
sys.exit("Good-bye.\n")
break
elif continueDel.strip().upper() != "Y":
print "Please answer with y or n"
else:
projPathAtRemote = raw_input("Please input the name of the project which you want to wipe out: ")
# #########################################
if pid in [1, 2]:
projPathAtLocal = os.environ["HOME"] + "/MyProjects_" + secId + "/private" + "/" + ProjToBeUnjoind
else:
projPathAtLocal = os.environ["HOME"] + "/MyProjects_" + secId + "/shared" + "/" + ProjToBeUnjoind
homePath = os.environ["HOME"]
os.chdir(os.environ["HOME"])
# Initialize as in start.project #####
startprojectXML = r"//genomics/lib/start.project/start.project.xml"
BIOINFOprojRootPath = r"//genomics/Projects"
BIOSTATprojRootPath = r"/proj/BIOSTAT/Projects"
USERprojRootPathPre = r"MyProjects"
SHAREDPATH = r"shared"
PRIVATEPATH = r"private"
continueAsk = 0
while continueAsk == 0:
projExist = "No"
if not (ProjToBeUnjoind == ""):
cask = 0
while cask == 0:
string1 = "The project contents of '%s' will be purged. Are you sure ?! y/n: " % (ProjToBeUnjoind)
AreYouSure = raw_input(string1)
if AreYouSure.strip().upper() == "Y":
print "\nDestorying Project. Please wait... \n ......\n"
continueAsk = 1
break
elif AreYouSure.strip().upper() == "N":
# print "Good-bye"
continueAsk = 1
print "\n Good-bye.\n"
sys.exit()
# break
else:
print "Please answer with y or n"
else:
print "\nThere is no project as your input. \nPlease verify the directory path and the project name to be wiped out.\n" # (\'%s\')%(ProjToBeUnjoindRawInput)
while True:
continueDel = raw_input("Do you wan to specify another project to wipe out? y/n: ")
print "\n"
if continueDel.strip().upper() == "Y":
break
elif continueDel.strip().upper() == "N":
print "Good-bye"
continueAsk = 1
sys.exit()
break
else:
print "Please answer with y or n"
memberList = []
if os.path.exists(projPathAtRemote):
for (basepath, children) in walktree(projPathAtRemote, False):
for child in children:
DirFile = os.path.join(basepath, child)
if os.path.islink(DirFile) and (not os.path.exists(os.path.realpath(DirFile))): # dead link
DirFile = os.path.dirname(os.path.join(basepath, child))
folderOwner = pwd.getpwuid(os.stat(DirFile)[4])[0]
if os.environ["USER"] != folderOwner:
GidOfjoinProjFolder = os.stat(projPathAtRemote)[5]
if GidOfjoinProjFolder in os.getgroups():
if (not (oct(os.stat(DirFile)[stat.ST_MODE] & 0777)[2] in ["7", "6", "2", "3"])) or (
not (oct(os.stat(DirFile)[stat.ST_MODE] & 0777)[3] in ["7", "6", "2", "3"])
):
if not (folderOwner in memberList):
print DirFile
memberList.append(folderOwner)
else:
print "%s, which is belong to %s, is not allowed to be deleted." % (
DirFile,
userName(folderOwner)[1] + userName(folderOwner)[2],
)
sys.exit()
elif (oct(os.stat(DirFile)[stat.ST_MODE] & 0777)[2] != "7") or (
oct(os.stat(DirFile)[stat.ST_MODE] & 0777)[3] != "7"
):
unlock = 'chmod ugo=rwx "%s"' % (DirFile)
os.system(unlock)
if len(memberList) >= 1:
members = ""
for member in memberList:
memberName = userName(member)[1] + " " + userName(member)[2]
members = memberName + ", " + members
members = members.rstrip(", ")
print 'The project can not be wiped out at this time.\nThere are still members in this project.\nPlease ask "%s" to unjoin project first.' % (
members
)
sys.exit()
# shared project delete
if 3 > 2:
if os.path.islink(projPathAtLocal):
os.remove(projPathAtLocal)
if os.path.exists(homePath + "/.mailboxlist"):
UnjoinMailSub(ProjToBeUnjoind, pid, secIdN, ".mailboxlist")
if os.path.exists(homePath + "/.subscriptions"):
UnjoinMailSub(ProjToBeUnjoind, pid, secIdN, ".subscriptions")
if secId == "BIOINFO":
projRoot0 = "//genomics"
elif secId == "BIOSTAT":
projRoot0 = "/proj/BIOSTAT"
if pid == 3:
pathToXML = projPathAtRemote + "/.common/" + ".proj_info.xml"
elif pid in [1, 2]:
pathToXML = projPathAtRemote + "/.proj_info.xml"
if os.path.exists(pathToXML):
xmldoc = minidom.parse(pathToXML)
cNodes = xmldoc.childNodes
projNum = cNodes[0].getElementsByTagName("projNum")
projNameP = projPathInfo[3]
projInfoFileName = os.path.basename((projNum)[0].firstChild.nodeValue.strip())
relativePathtoXML = projPathInfo[3]
XMLLink = os.path.join(
projRoot0, "Projects/.projInfo", (os.path.join(projNameP, projInfoFileName)).replace("/", "=>")
)
try:
tempstring = 'rm "%s"' % (XMLLink)
os.remove(XMLLink)
except:
aa = 0
if pid == 3:
PublicFolder = projRoot0 + "/Public/.projects/" + ProjToBeUnjoind
if os.path.exists(PublicFolder):
removePublic = 'rm -R -f "%s"' % (PublicFolder)
os.system(removePublic)
localMail = projPathAtLocal.replace(os.environ["HOME"], os.environ["HOME"] + "/mail")
if os.path.exists(localMail):
removeMail = 'rm -R -f "%s"' % (localMail)
os.system(removeMail)
projPathAtRemoteAP = projPathInfo[4]
projNameA = projPathInfo[2]
moveMain = 'rm -R -f "%s"' % (projPathAtRemote)
os.system(moveMain)
projPathAtLocal = projPathInfo[9]
localPathPrefix = projPathInfo[8]
localMail = projPathAtLocal.replace(os.environ["HOME"], os.path.join(os.environ["HOME"], "mail"), 1)
if pidType == "private":
snipTree(folderPathRaw=os.path.dirname(projPathAtLocal), stopRaw=localPathPrefix) # local main
snipTree(folderPathRaw=os.path.dirname(localMail), stopRaw=os.path.join(os.environ["HOME"], "mail"))
snipTree(folderPathRaw=projPathAtRemoteAP, stopRaw=pathPrefix)
else:
snipTree(folderPathRaw=os.path.dirname(projPathAtLocal), stopRaw=localPathPrefix) # local main
snipTree(folderPathRaw=os.path.dirname(localMail), stopRaw=os.path.join(os.environ["HOME"], "mail"))
snipTree(folderPathRaw=projPathAtRemoteAP, stopRaw=pathPrefix)
remotePublicRoot = pathPrefix.replace("/Projects/shared", "/Public/.projects", 1)
remotePublic = projPathAtRemoteAP.replace(pathPrefix, remotePublicRoot, 1)
snipTree(folderPathRaw=remotePublic, stopRaw=remotePublicRoot)
print "Wipeout operation is completed. Good-bye.\n"
def delProj(projPathAtRemote):
import os,sys,pwd,stat
from xml.dom import minidom
from osWalk import walktree
from userName import userName
from UnjoinMail import UnjoinMailSub
from pathInfo import pathInfo_d,pathInfo_ks
from unjoinProj import unjoinProj
from snipTree import snipTree
##################################
projPathInfo=pathInfo_d(projPathAtRemote)
# pathInfo: pathOutput=(pathAbs,projName,projNameA,projNameP,projNameAP,pathPrefix,secId,pidType)
# 0 1 2 3 4 5 6 7
# -2 -1
secId=projPathInfo[6]
pidType=projPathInfo[7]
projName=projPathInfo[1]
projNameP=projPathInfo[3]
pathPrefix=projPathInfo[5]
if pidType=='private':
pid=1
elif pidType=='shared':
pid=3
else: sys.exit("Wrong project type, contact support")
if secId=='BIOSTAT':
secIdN=1
elif secId=='BIOINFO':
secIdN=2
else: sys.exit("Wrong section ID, contact support")
if projPathInfo[7]=='shared':
print "\nYou are going to delete a project with the following parameters:"
print " Section : %s" %(projPathInfo[6])
print " Project Type : %s" %(projPathInfo[7])
print " Local Project Path : %s" %(projPathInfo[9])
print "Remote Project Path : %s\n" %(projPathInfo[0])
pathVerify=raw_input("Is the above information correct [y] (y/n) ? " )
pathVerify=pathVerify.upper()
#print pathVerify
while not (pathVerify in ["","Y","N","YES","NO"]):
print "Please answer with \"y\" or \"n\" "
pathVerify=raw_input("Are these correct [y] (y/n)? " )
pathVerify=pathVerify.upper()
if pathVerify in ["N","NO"]:
sys.exit("Please change to your home directory and rerun the start.project.")
###########################################
projPathAtRemote=projPathInfo[0]
ProjToBeUnjoind=projPathInfo[1]
###########################################
while not os.path.exists(projPathAtRemote):
print "\nThere is no project as your input (\'%s\'). \nPlease verify the project name and directory path.\n" %(projPathAtRemote)
continueDel=raw_input("Do you wan to specify another project to delete? y/n: ")
print "\n"
if (continueDel.strip().upper() == 'N'):
sys.exit("Good-bye.\n")
break
elif (continueDel.strip().upper() != 'Y'):
print "Please answer with y or n"
else:
projPathAtRemote = raw_input("Please input the name of the project which you want to delete: ")
############################################
# get local proj path ###
if pid in [1,2]:
projPathAtLocal=os.environ['HOME']+'/MyProjects_'+secId+'/private'+'/'+ProjToBeUnjoind
else:
projPathAtLocal=os.environ['HOME']+'/MyProjects_'+secId+'/shared'+'/'+ProjToBeUnjoind
homePath=os.environ['HOME']
os.chdir(os.environ['HOME'])
# Initialize as in the start.project #######
startprojectXML = r'//genomics/lib/start.project/start.project.xml'
BIOINFOprojRootPath = r'//genomics/Projects'
BIOSTATprojRootPath = r'/proj/BIOSTAT/Projects'
USERprojRootPathPre = r'MyProjects'
SHAREDPATH = r'shared'
PRIVATEPATH = r'private'
###############
if pidType == 'private':
try:
unjoinProj(projPathAtRemote=projPathAtRemote,pattern='non-verbose',pd='Tt')
except:
sys.exit("Errors. Pleasee contact support.")
print "Deleting.... Please wait.\n .... "
sys.exit("Delete completed. Good bye.")
################
################
continueAsk=0
while continueAsk==0:
projExist="No"
if ( not(ProjToBeUnjoind=='')) :
cask=0
while cask==0:
string1='Are you sure to delete the whole project \'%s\' y/n ?: ' %(ProjToBeUnjoind)
AreYouSure=raw_input(string1)
if (AreYouSure.strip().upper() == 'Y'):
print "\nDeleting. Please wait... \n ......\n"
continueAsk=1
break
elif (AreYouSure.strip().upper() == 'N'):
continueAsk=1
print '\n Good-bye.\n'
sys.exit()
else:
print "Please answer with y or n"
else:
print "\nThere is no project as your input. \nPlease verify the directory path and the project name to be deleted.\n" #(\'%s\')%(ProjToBeUnjoindRawInput)
while True:
continueDel=raw_input("Do you wan to specify another project to delete? y/n: ")
print "\n"
if (continueDel.strip().upper() == 'Y'):
break
elif (continueDel.strip().upper() == 'N'):
print "Good-bye"
continueAsk=1
sys.exit()
break
else:
print "Please answer with y or n"
#############################################
DirFileInfo=[]
memberList=[]
if os.path.exists(projPathAtRemote):
for (basepath, children) in walktree(projPathAtRemote,False):
for child in children:
DirFile=os.path.join(basepath, child)
folderOwner=pwd.getpwuid(os.stat(DirFile)[4])[0] #lstat ==>stat
if os.environ["USER"]!=folderOwner:
GidOfjoinProjFolder=os.stat(projPathAtRemote)[5]
if (GidOfjoinProjFolder in os.getgroups()):
if (not (oct(os.stat(DirFile)[stat.ST_MODE] & 0777)[2] in ['7','6','3','2'])) and (not (oct(os.stat(DirFile)[stat.ST_MODE] & 0777)[3] in ['7','6','3','2'])):
if not(folderOwner in memberList):
#print DirFile
DirFileInfo.append(DirFile)
memberList.append(folderOwner)
else:
print "%s, which is belong to %s, is not allowed to be deleted." %(DirFile, userName(folderOwner)[1]+userName(folderOwner)[2])
sys.exit()
elif (oct(os.lstat(DirFile)[stat.ST_MODE] & 0777)[1:3]!=['7','7','7']):
unlock='chmod ugo=rwx \"%s\"' %(DirFile)
os.system(unlock)
if os.environ["USER"]==pwd.getpwuid(os.stat(projPathAtRemote)[4])[0]:
if (oct(os.lstat(projPathAtRemote)[stat.ST_MODE] & 0777)[1:3]!=['7','7','7']):
unlock='chmod ugo=rwx \"%s\"' %(projPathAtRemote)
os.system(unlock)
if len(memberList)>=1:
members=''
for member in memberList:
memberName=userName(member)[1]+' '+userName(member)[2]
members=memberName+', '+members
members=members.rstrip(', ')
print "The project can not be deleted at this time.\nThere are still members in this project.\nPlease ask \"%s\" to unjoin project first." %(members)
sys.exit()
# shared project delete
if 3>2:
if os.path.islink(projPathAtLocal):
os.remove(projPathAtLocal)
if os.path.exists(homePath+'/.mailboxlist'):
UnjoinMailSub(ProjToBeUnjoind,pid,secIdN,'.mailboxlist')
if os.path.exists(homePath+'/.subscriptions'):
UnjoinMailSub(ProjToBeUnjoind,pid,secIdN,'.subscriptions')
if secId=='BIOINFO':
projRoot0='//genomics'
elif secId=='BIOSTAT':
projRoot0='/proj/BIOSTAT'
pathToXML=projPathAtRemote+'/.common/'+'.proj_info.xml'
if os.path.exists(pathToXML):
xmldoc=minidom.parse(pathToXML)
cNodes=xmldoc.childNodes
projNum=cNodes[0].getElementsByTagName("projNum")
projNameP=projPathInfo[3]
projInfoFileName=os.path.basename((projNum)[0].firstChild.nodeValue.strip())
relativePathtoXML=projPathInfo[3]
XMLLink=os.path.join(projRoot0,'Projects/.projInfo',projInfoFileName.replace('/','=>'))
try:
os.remove(XMLLink)
os.remove('.'+XMLLink)
except:
aa=0
PublicFolder=projRoot0+'/Public/.projects/'+ProjToBeUnjoind
if os.path.exists(PublicFolder):
removePublic='rm -R -f \"%s\"' %(PublicFolder)
os.system(removePublic)
localMail=projPathAtLocal.replace(os.environ['HOME'],os.environ['HOME']+'/mail')
if os.path.exists(localMail):
removeMail='rm -R -f \"%s\"' %(localMail)
os.system(removeMail)
projPathAtRemoteAP=projPathInfo[4]
projNameA=projPathInfo[2]
if projPathAtRemote!=os.path.join(projPathAtRemoteAP,'.'+projInfoFileName):
moveMain='mv \"%s\" \"%s\"' %(projPathAtRemote, os.path.join(projPathAtRemoteAP,'.'+projInfoFileName))
os.system(moveMain)
newDeletedName=(os.path.join(projNameP,projInfoFileName)).replace('/','=>')
move2deleted=os.path.join(os.path.dirname(pathPrefix),'.deleted',newDeletedName)
move2='mv \"%s\" \"%s\"' %(os.path.join(projPathAtRemoteAP,'.'+projInfoFileName),move2deleted)
os.system(move2)
projInfoLink=os.path.join(os.path.dirname(pathPrefix),'.projInfo',newDeletedName)
if os.path.exists(projInfoLink):
os.remove(projInfoLink)
projPathAtLocal= projPathInfo[9]
localPathPrefix=projPathInfo[8]
localMail=projPathAtLocal.replace(os.environ['HOME'],os.path.join(os.environ['HOME'],'mail'),1)
if pidType=='shared':
snipTree(folderPathRaw=os.path.dirname(projPathAtLocal), stopRaw=localPathPrefix) #local main
snipTree(folderPathRaw=os.path.dirname(localMail), stopRaw=os.path.join(os.environ['HOME'],'mail'))
snipTree(folderPathRaw=projPathAtRemoteAP, stopRaw=pathPrefix)
remotePublicRoot=pathPrefix.replace('/Projects/shared', '/Public/.projects',1)
remotePublic=projPathAtRemoteAP.replace(pathPrefix,remotePublicRoot,1)
snipTree(folderPathRaw=remotePublic, stopRaw=remotePublicRoot)
print "Delete completed. Good-bye."
# 1. update info in projInfo.xml: path of proj changed => projNum
# 2. update the sym link in /proj/BIOSTAT/Projects/.projInfo/...
# 4. Send emails to all users: 1.notice the moving 2. local files rewrite 3. member's Common file sys link rewrite.
# (member should have full rights for 2 & 3, since they are owned by members.)
# 3. self local file re-link
# 1 and 2 start here
currentMemberInfo=[]
try:
if pidType_old=='shared':
if oldisproj=='yes' and newisproj=='no':
if os.path.exists(pathAbs_new):
print "The new project place is not available for using. Choose ohter place to move to."
sys.exit()
sponsorId=pwd.getpwuid(os.lstat(pathAbs_old)[4])[0]
sponsorName=userName(sponsorId)[1]+' '+userName(sponsorId)[2]
if (os.environ["USER"]==sponsorId):
iscurrenmember=0
pathToXML=os.path.join(pathAbs_old,'.common','.proj_info.xml')
pathToXML_new=os.path.join(pathAbs_new,'.common','.proj_info.xml')
elif oldisproj=='no' and newisproj=='yes':
sponsorId=pwd.getpwuid(os.lstat(pathAbs_new)[4])[0]
sponsorName=userName(sponsorId)[1]+' '+userName(sponsorId)[2]
if (os.environ["USER"]!=sponsorId):
iscurrenmember=1
# also, not allow unjoined member to move project.
pathToXML=os.path.join(pathAbs_new,'.common','.proj_info.xml')
pathToXML_new=os.path.join(pathAbs_new,'.common','.proj_info.xml')
else:
if oldisproj=='yes' and newisproj=='yes':
print '''%s is an existed project. Please select other project path''' %(pathAbs_new)
def pathInfo_d(pathRaw):
import os,sys,pwd,stat
pathOutput=pathInfo_base(pathRaw)
pathabs=pathOutput[0]
pathPrefix=pathOutput[5]
projName=pathOutput[1]
secId=pathOutput[6]
pidType=pathOutput[7]
pathInfo_ks(pathOutput)
folderStatus=0
if (not os.path.isfile(os.path.join(pathabs,'.proj_info.xml'))) \
and ((not os.path.isfile(os.path.join(pathabs,'.common','.proj_info.xml'))) \
and (not os.path.exists(os.path.join(pathabs,'.public')))):
print '''%s is not an existed project. \nPlease check.''' %(pathabs)
folderStatus=1
sys.exit()
if secId=='BIOSTAT':
grpName='staff'
grpId=10 #50 #10 #20
elif secId=='BIOINFO':
grpName=secId
grpId=301 #301 #301
else: sys.exit("Wrong secId, contact support")
if not os.path.exists(pathPrefix):
os.makedirs(pathPrefix,mode=0755) #only needed for private proj
os.chown(pathPrefix,-1,grpId)
if (not(grpId in os.getgroups())):
print "You do not have group permission to write in the path."
sys.exit()
dir0=os.path.dirname(projName)
dirsRaw=[dir0]
while dir0!='':
dir0=os.path.dirname(dir0)
if dir0!='':
dirsRaw.append(dir0)
dirsRaw.sort()
dirs=tuple(dirsRaw)
for item in dirs:
dirCurrent=os.path.join(pathPrefix, item)
if not os.path.exists(dirCurrent):
print "The proj path does nor exist. Plese verify and try again."
else:
if os.path.isfile(os.path.join(dirCurrent,'.proj_info.xml')):
print '''%s is an existed project. \nUsing the same name as both project name and project path is not allowed.\nPlease select other project path''' %(dirCurrent)
folderStatus=1
continue
if os.path.isfile(os.path.join(dirCurrent,'.common','.proj_info.xml')) \
or os.path.exists(os.path.join(dirCurrent,'.public')):
print '''%s is an existed project. \nUsing the same name as both project name and project path is not allowed.\nPlease select other project path''' %(dirCurrent)
folderStatus=1
continue
folderOwner=pwd.getpwuid(os.lstat(pathabs)[4])[0]
folderGid=os.stat(pathabs)[5]
if os.environ["USER"]!=folderOwner:
if (folderGid!=grpId) or (oct(os.stat(pathabs)[stat.ST_MODE] & 0777)[2]!='7'):
userNameInfo=userName(folderOwner)
print "You do not have permission to write in %s.\nPlease ask %s %s, who is the owner of this folder, to reset permission for you. " %(pathabs,userNameInfo[1],userNameInfo[2]) #grpId and group permission problem ==>exit
folderStatus=1
os.exit()
else:
if (oct(os.stat(pathabs)[stat.ST_MODE] & 0777)[1:2]!=['7','7']):
tempstring='chmod ug+rwx \"%s\"' %(dirCurrent) # inherit group ID in this path
os.system(tempstring)
if folderGid!=grpId:
os.chown(pathabs,-1,grpId)
if pidType=='private':
tempstring='chmod -R go=rx \"%s\"' %(pathPrefix)
os.system(tempstring)
if folderStatus==1:
sys.exit()
else:
return pathOutput
def pathInfo(pathRaw):
import os,sys,pwd,stat
from userName import userName
pathOutput=pathInfo_base(pathRaw)
# Input pathprefix and projName(relative path to pathPrefix)
# pathInfo: pathOutput=(pathAbs,projName,projNameA,projNameP,projNameAP,pathPrefix,secId,pidType,localPathPrefix,projPathAtLocal)
# 0 1 2 3 4 5 6 7 8 9
# -2 -1
pathabs=pathOutput[0]
pathPrefix=pathOutput[5]
projName=pathOutput[1]
secId=pathOutput[6]
pidType=pathOutput[7]
projNameP=pathOutput[3]
folderStatus=0
if os.path.isfile(os.path.join(pathabs,'.proj_info.xml')):
print '''%s is an existed project. \nUsing the same name as both project name and project path is not allowed.\nPlease select other project path''' %(pathabs)
folderStatus=1
sys.exit()
if os.path.isfile(os.path.join(pathabs,'.common','.proj_info.xml')) \
or os.path.exists(os.path.join(pathabs,'.public')):
print '''%s is an existed project. \nUsing the same name as both project name and project path is not allowed.\nPlease select other project path''' %(pathabs)
folderStatus=1
sys.exit()
if secId=='BIOSTAT':
grpName='staff'
grpId=10 #50 #10 #20
elif secId=='BIOINFO':
grpName=secId
grpId=301 #301 #301
else: sys.exit("Wrong secId, contact support")
if not os.path.exists(pathPrefix):
os.makedirs(pathPrefix,mode=0755)
os.chown(pathPrefix,-1,grpId)
if (not(grpId in os.getgroups())):
print "You do not have group permission to write in the path."
sys.exit()
dir0=os.path.dirname(projName)
dirsRaw=[dir0]
while dir0!='':
dir0=os.path.dirname(dir0)
if dir0!='':
dirsRaw.append(dir0)
dirsRaw.sort()
dirs=tuple(dirsRaw)
for item in dirs:
dirCurrent=os.path.join(pathPrefix, item)
if not os.path.exists(dirCurrent):
tempstring='mkdir -m0775 \"%s\"' %(dirCurrent)
os.system(tempstring)
os.chown(dirCurrent,-1,grpId)
tempstring='chmod ug+s \"%s\"' %(dirCurrent)
os.system(tempstring)
else:
if os.path.isfile(os.path.join(dirCurrent,'.proj_info.xml')):
print '''%s is an existed project. \nUsing the same name as both project name and project path is not allowed.\nPlease select other project path''' %(dirCurrent)
folderStatus=1
continue
if os.path.isfile(os.path.join(dirCurrent,'.common','.proj_info.xml')) \
or os.path.exists(os.path.join(dirCurrent,'.public')):
print '''%s is an existed project. \nUsing the same name as both project name and project path is not allowed.\nPlease select other project path''' %(dirCurrent)
folderStatus=1
continue
folderOwner=pwd.getpwuid(os.lstat(dirCurrent)[4])[0]
folderGid=os.stat(dirCurrent)[5]
if os.environ["USER"]!=folderOwner:
if (folderGid!=grpId) or (oct(os.stat(dirCurrent)[stat.ST_MODE] & 0777)[2]!='7'):
userNameInfo=userName(folderOwner)
print "You do not have permission to write in %s.\nPlease ask %s %s, who is the owner of this folder, to reset permission for you. " %(dirCurrent,userNameInfo[1],userNameInfo[2]) #grpId and group permission problem ==>exit
folderStatus=1
continue
else:
if (oct(os.stat(dirCurrent)[stat.ST_MODE] & 0777)[1:2]!=['7','7']):
tempstring='chmod ug+rwx \"%s\"' %(dirCurrent)
os.system(tempstring)
if folderGid!=grpId:
os.chown(dirCurrent,-1,grpId)
if pidType=='shared':
if secId=='BIOSTAT':
publicPrefix='/proj/BIOSTAT/Public/.projects'
projInfoPrefix='/proj/BIOSTAT/Projects/.projInfo'
elif secId=='BIOINFO':
publicPrefix='//genomics/Public/.projects'
projInfoPrefix='//genomics/Projects/.projInfo'
old_umask=os.umask(0002)
if not os.path.exists(publicPrefix):
os.makedirs(publicPrefix,mode=0775)
os.chown(publicPrefix,-1,grpId)
umask_back=os.umask(old_umask)
pubdirs=os.path.join(publicPrefix,projNameP)
dir0=projNameP
dirsRaw=[dir0]
while dir0!='':
dir0=os.path.dirname(dir0)
if dir0!='':
dirsRaw.append(dir0)
dirsRaw.sort()
dirs=tuple(dirsRaw)
prefixs=publicPrefix
for item in dirs:
dirCurrent=os.path.join(prefixs, item)
if not os.path.exists(dirCurrent):
tempstring='mkdir -m0775 \"%s\"' %(dirCurrent)
os.system(tempstring)
os.chown(dirCurrent,-1,grpId)
tempstring='chmod -R ug+s \"%s\"' %(dirCurrent)
os.system(tempstring)
else:
folderOwner=pwd.getpwuid(os.lstat(dirCurrent)[4])[0]
folderGid=os.stat(dirCurrent)[5]
if os.environ["USER"]!=folderOwner:
if (folderGid!=grpId) or (oct(os.stat(dirCurrent)[stat.ST_MODE] & 0777)[2]!='7'):
userNameInfo=userName(folderOwner)
print "You do not have permission to write in %s.\nPlease ask %s %s, who is the owner of this folder, to reset permission for you. " %(dirCurrent,userNameInfo[1],userNameInfo[2]) #grpId and group permission problem ==>exit
folderStatus=1
continue
else:
if (oct(os.stat(dirCurrent)[stat.ST_MODE] & 0777)[1:2]!=['7','7']):
tempstring='chmod ug+rwx \"%s\"' %(dirCurrent)
os.system(tempstring)
if folderGid!=grpId:
os.chown(dirCurrent,-1,grpId)
tempstring='chmod ug+s \"%s\"' %(dirCurrent)
os.system(tempstring)
if pidType=='private':
tempstring='chmod -R go=rx \"%s\"' %(pathPrefix)
os.system(tempstring)
if folderStatus==1:
sys.exit()
else:
return pathOutput
