def handle(self):
db = self.__db
cursor = self.__cursor
form = cgi.FieldStorage(keep_blank_values="True")
uHandler = UserHandler(db, cursor)
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
if form.has_key("username"):
# store the user ID for use throughout the session; add to other views in addition to create in PHP
currUname = form.getvalue("username")
currUser = uHandler.getUserByDescription(currUname)
Session.setUser(currUser)
elif form.has_key("curr_user_id"):
currUID = form.getvalue("curr_user_id")
currUser = uHandler.getUserByID(currUID)
Session.setUser(currUser)
if form.has_key("create_project"):
self.createProject(form)
elif form.has_key("modify_project"):
self.modifyProject(form)
elif form.has_key("save_project"):
self.saveProject(form)
elif form.has_key("cancel_project"):
self.cancelModification(form)
elif form.has_key("delete_project"):
self.deleteProject(form)
elif form.has_key("view_project"):
self.printProjectInfo(form)
elif form.has_key("view_packet"):
# go to project view from User detailed view
self.viewPacket(form)
# Oct. 12, 2010
elif form.has_key("search_project_by_keyword"):
self.findPacket(form)
cursor.close()
db.close()
def handle(self):
db = self.__db
cursor = self.__cursor
form = cgi.FieldStorage(keep_blank_values="True")
uHandler = UserHandler(db, cursor)
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
if form.has_key("username"):
# store the user ID for use throughout the session; add to other views in addition to create in PHP
currUname = form.getvalue("username")
currUser = uHandler.getUserByDescription(currUname)
Session.setUser(currUser)
elif form.has_key("curr_user_id"):
currUID = form.getvalue("curr_user_id")
currUser = uHandler.getUserByID(currUID)
Session.setUser(currUser)
if form.has_key("create_project"):
self.createProject(form)
elif form.has_key("modify_project"):
self.modifyProject(form)
elif form.has_key("save_project"):
self.saveProject(form)
elif form.has_key("cancel_project"):
self.cancelModification(form)
elif form.has_key("delete_project"):
self.deleteProject(form)
elif form.has_key("view_project"):
self.printProjectInfo(form)
elif form.has_key("view_packet"):
# go to project view from User detailed view
self.viewPacket(form)
# Oct. 12, 2010
elif form.has_key("search_project_by_keyword"):
self.findPacket(form)
cursor.close()
db.close()
def handle(self):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
mail_server = self.__mail_server # August 19, 2011
mail_admin = self.__mail_admin # August 19, 2011
clone_request = self.__clone_request
form = cgi.FieldStorage(keep_blank_values="True")
uHandler = UserHandler(db, cursor)
# print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
# print # DITTO
# print `form`
if form.has_key("curr_username"):
# store the user ID for use throughout the session; add to other views in addition to create in PHP
currUname = form.getvalue("curr_username")
currUser = uHandler.getUserByDescription(currUname)
Session.setUser(currUser)
elif form.has_key("curr_user_id"):
currUID = form.getvalue("curr_user_id")
currUser = uHandler.getUserByID(currUID)
Session.setUser(currUser)
if form.has_key("add_user"):
self.addUser(form)
elif form.has_key("modify_user"):
self.modifyUser(form)
elif form.has_key("cancel_user"):
self.cancelUserModification(form)
elif form.has_key("save_user"):
self.saveUser(form)
elif form.has_key("delete_user"):
self.deleteUser(form)
elif (
form.has_key("view_user")
and form.getvalue("view_user") != ""
and not form.has_key("modify_lab")
and not form.has_key("delete_lab")
):
self.viewUser(form)
# Nov. 17/07 - Personal user page
elif (
form.has_key("view_user")
and form.getvalue("view_user") == ""
and not form.has_key("modify_lab")
and not form.has_key("delete_lab")
):
self.printUserInfo("view", currUser)
elif form.has_key("add_lab"):
self.addLab(form)
elif form.has_key("view_lab"):
self.viewLab(form)
elif form.has_key("modify_lab"):
self.modifyLab(form)
elif form.has_key("save_lab"):
self.saveLab(form)
elif form.has_key("cancel_lab"):
self.cancelLabModification(form)
elif form.has_key("delete_lab"):
self.deleteLab(form)
elif form.has_key("bug_report"):
self.submitBug(form)
elif form.has_key("send_order"):
######################################################################
# CHANGE SERVER NAME AND EMAIL TO YOUR LOCAL CREDENTIALS
######################################################################
userID = form.getvalue("curr_user_id")
userDescr = form.getvalue("curr_username")
from_email = uHandler.findEmail(userID)
if not from_email:
from_email = userDescr
to_email = clone_request
email_subject = userDescr + ": Clone Request"
f_in = form.getvalue("outputContent")
infile = open(f_in, "rb")
msg = email.MIMEMultipart.MIMEMultipart()
# msg.attach(email.MIMEText.MIMEText(infile.read())) # no, this attaches plain text
msg["Subject"] = email_subject
part = email.MIMEBase.MIMEBase("application", "octet-stream")
part.set_payload(infile.read())
email.Utils.base64.standard_b64encode(infile.read())
part.add_header("Content-Disposition", 'attachment; filename="%s"' % os.path.basename(f_in))
msg.attach(part)
server = smtplib.SMTP(mail_server)
server.set_debuglevel(1)
# Send a request to your clone request address
server.sendmail(from_email, to_email, msg.as_string())
# AND send a copy to the user (change the subject)
# msg['Subject'] = "Clone request confirmation" # doesn't change, investigate later
# Return email text changed March 31/08
#######################################
# CHANGE TEXT AS NEEDED
#######################################
msg.attach(
email.MIMEText.MIMEText(
"This is a copy of your clone request. Please retain for your records. You will be notified by e-mail when your clone is ready."
)
)
server.sendmail(to_email, from_email, msg.as_string())
server.quit()
# Method 2
# sendmail = "/usr/sbin/sendmail"
# o = os.popen("%s -t" % sendmail,"w")
# o.write("To: %s\r\n" % to_email)
# if from_email:
# o.write("From: %s\r\n" % from_email)
# o.write("Subject: %s\r\n" % email_subject)
# o.write("\r\n")
# o.write("%s\r\n" % msg)
# o.close()
os.remove(f_in) # delete the file from /tmp dir
utils.redirect(hostname + "User.php?View=8&Sent=1")
# June 1, 2010: Automated password reset
elif form.has_key("reset_pw"):
# change June 2, 2010: Don't enter email, rather, ask users to enter their username - more secure
# to_email = form.getvalue("email")
from_email = mail_admin
# success = True
chars = string.letters + string.digits
new_passwd = ""
for i in range(10):
new_passwd += choice(chars)
# reset it in the database
if form.has_key("uName"):
u_name = form.getvalue("uName")
userID = uHandler.findUserIDByUsername(u_name)
if userID > 0:
u_descr = uHandler.findDescription(userID)
to_email = uHandler.findEmail(userID)
uHandler.setUserPropertyValue(userID, "password", new_passwd)
email_subject = "OpenFreezer Password Change"
msg = email.MIMEMultipart.MIMEMultipart()
# msg.attach(email.MIMEText.MIMEText(infile.read())) # no, this attaches plain text
msg["Subject"] = email_subject
###################################
# CHANGE TEXT AS NEEDED
###################################
msg.attach(
email.MIMEText.MIMEText(
"Dear "
+ u_descr
+ ",\n\nYour password for OpenFreezer has been changed.\n\nYour temporary new password is: "
+ new_passwd
+ ".\n\nPlease change the temporary password as soon as you log into the system.\n\nYour username for OpenFreezer is '"
+ u_name
+ "'.\n\nFor any questions, please refer to http://openfreezer.org. \n\nSincerely,\nOpenFreezer support team.\n--------------------------------\nThis is an automatically generated e-mail message. Please do not reply to this e-mail. All questions should be directed to your local administrator."
)
)
server = smtplib.SMTP(mail_server)
server.set_debuglevel(1)
server.sendmail(from_email, to_email, msg.as_string())
server.quit()
utils.redirect(hostname + "User.php?View=6&Reset=1&uid=" + ` userID `)
else:
# retry by description
if form.has_key("uDesc"):
u_descr = form.getvalue("uDesc")
# but account for whitespace
toks = u_descr.split(" ")
tmp_descr = ""
for tok in toks:
tmp_descr += tok.strip() + " "
# strip extra whitespace from end
tmp_descr = tmp_descr.strip()
userID = uHandler.findUserIDByDescription(tmp_descr)
if userID > 0:
u_name = uHandler.findUsername(userID)
to_email = uHandler.findEmail(userID)
uHandler.setUserPropertyValue(userID, "password", new_passwd)
email_subject = "OpenFreezer Password Change"
msg = email.MIMEMultipart.MIMEMultipart()
# msg.attach(email.MIMEText.MIMEText(infile.read())) # no, this attaches plain text
msg["Subject"] = email_subject
##############################
# CHANGE TEXT AS NEEDED
##############################
msg.attach(
email.MIMEText.MIMEText(
"Dear "
+ u_descr
+ ",\n\nYour password for OpenFreezer has been changed.\n\nYour temporary new password is: "
+ new_passwd
+ ".\n\nPlease change the temporary password as soon as you log into the system.\n\nYour username for OpenFreezer is '"
+ u_name
+ "'.\n\nPlease refer to http://openfreezer.org for additional support.\n\nSincerely,\nOpenFreezer support team.\n--------------------------------\nThis is an automatically generated e-mail message. Please do not reply to this e-mail. All questions should be directed to <a href='mailto:"
+ mail_admin
+ "'>"
+ mail_admin
+ "</a>"
)
)
server = smtplib.SMTP(mail_server)
server.set_debuglevel(1)
server.sendmail(from_email, to_email, msg.as_string())
server.quit()
utils.redirect(hostname + "User.php?View=6&Reset=1&uid=" + ` userID `)
else:
utils.redirect(hostname + "User.php?View=6&Reset=0")
else:
utils.redirect(hostname + "User.php?View=6&Reset=0")
else:
utils.redirect(hostname + "User.php?View=6&Reset=0")
cursor.close()
db.close()
def update():
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
form = cgi.FieldStorage(keep_blank_values="True")
print "Content-type:text/html" # REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
print # DITTO
#print `form`
# Aug 29/07
uHandler = UserHandler(db, cursor)
if form.has_key("curr_username"):
# store the user ID for use throughout the session; add to other views in addition to create in PHP
currUname = form.getvalue("curr_username")
currUser = uHandler.getUserByDescription(currUname)
Session.setUser(currUser)
#else: # debug
#currUname = 'Administrator'
#currUser = uHandler.getUserByDescription(currUname)
#Session.setUser(currUser)
if form.has_key("cloning_method"):
cloning_method = form.getvalue("cloning_method")
#else: # debug
#cloning_method = '1'
# Handlers and mappers
rHandler = ReagentHandler(db, cursor)
#sHandler = SystemSetHandler(db, cursor)
pHandler = ReagentPropertyHandler(db, cursor)
raHandler = ReagentAssociationHandler(db, cursor)
aHandler = AssociationHandler(db, cursor)
dnaHandler = DNAHandler(db, cursor)
commHandler = CommentHandler(db, cursor)
protHandler = ProteinHandler(db, cursor)
propMapper = ReagentPropertyMapper(db, cursor)
assocMapper = ReagentAssociationMapper(db, cursor)
# August 29/07: Restrict creation by user and project access
packetHandler = ProjectDatabaseHandler(db, cursor)
########################################################
# Various maps
########################################################
prop_Alias_ID_Map = propMapper.mapPropAliasID() # (propAlias, propID) - e.g. ('insert_type', '48') --> represents 'type of insert' property
prop_Name_Alias_Map = propMapper.mapPropNameAlias() # (propName, propAlias)
prop_Name_ID_Map = propMapper.mapPropNameID() # (prop name, prop id)
# Restriction sites
fpcs_prop_id = pHandler.findPropID("5' cloning site")
tpcs_prop_id = pHandler.findPropID("3' cloning site")
newFivePrime = form.getvalue("fpcs")
newThreePrime = form.getvalue("tpcs")
gatewaySites = ['attb', 'attl', 'attp', 'attr'] # nov. 16/07
# resulting sequence
newSeq = ""
# Fetch projects the user has AT LEAST Read access to (i.e. if he is explicitly declared a Writer on a project but not declared a Reader, include that project, plus all public projects)
currReadProj = packetHandler.findMemberProjects(currUser.getUserID(), 'Reader')
currWriteProj = packetHandler.findMemberProjects(currUser.getUserID(), 'Writer')
publicProj = packetHandler.findAllProjects(isPrivate="FALSE")
# list of Packet OBJECTS
currUserWriteProjects = utils.unique(currReadProj + currWriteProj + publicProj)
uPackets = []
for p in currUserWriteProjects:
uPackets.append(p.getNumber())
# Get project IDs of parents
packetPropID = pHandler.findPropID("packet id")
# August 29/07: Need to verify parent project access AND (Sept. 12/07) reconstruct the sequence IFF parent values are changed
newSeq = ""
# Fetch projects the user has AT LEAST Read access to (i.e. if he is explicitly declared a Writer on a project but not declared a Reader, include that project, plus all public projects)
currReadProj = packetHandler.findMemberProjects(currUser.getUserID(), 'Reader')
currWriteProj = packetHandler.findMemberProjects(currUser.getUserID(), 'Writer')
publicProj = packetHandler.findAllProjects(isPrivate="FALSE")
# list of Packet OBJECTS
currUserWriteProjects = utils.unique(currReadProj + currWriteProj + publicProj)
uPackets = []
for p in currUserWriteProjects:
uPackets.append(p.getNumber())
# Get project IDs of parents
packetPropID = pHandler.findPropID("packet id")
if form.has_key("PV"):
pvVal = form.getvalue("PV")
if len(pvVal) > 0:
pvID = rHandler.convertReagentToDatabaseID(pvVal)
try:
pvProjectID = int(rHandler.findSimplePropertyValue(pvID, packetPropID))
pvSeqID = rHandler.findDNASequenceKey(pvID) # get sequence for reconstitution later
except TypeError:
#pvProjectID = 0
e = PVProjectAccessException("You are not authorized to use this Parent Vector, since you do not have Read access to its project.")
print `e.err_code()`
else:
e = UnknownPVIDException("Unknown Parent Vector value")
print `e.err_code()`
return
# else don't do anything, maybe want to delete parents!!!
#else:
#e = MissingPVException("No Parent Vector provided")
#print `e.err_code()`
if pvProjectID > 0 and currUser.getCategory() != 'Admin' and pvProjectID not in uPackets:
e = PVProjectAccessException("Not authorized to access parent")
print `e.err_code()`
return
if cloning_method == '1':
# Non-recombination vector - Get the Insert
if form.has_key("I"):
insertVal = form.getvalue("I")
if len(insertVal) > 0:
insertID = rHandler.convertReagentToDatabaseID(insertVal)
insertSeqID = rHandler.findDNASequenceKey(insertID) # fetch Insert sequence for reconstitution later
try:
insertProjectID = int(rHandler.findSimplePropertyValue(insertID, packetPropID))
except TypeError:
#insertProjectID = 0
e = InsertProjectAccessException("You are not authorized to use this Insert, since you do not have Read access to its project.")
print `e.err_code()`
else:
#insertID = -1
#insertProjectID = 0
#print "Invalid Insert value"
e = UnknownInsertIDException("Unknown Insert value")
print `e.err_code()`
return
#else: # NO!!!!!!!!
#e = MissingInsertException("No Insert provided")
#print `e.err_code()`
if insertProjectID > 0 and currUser.getCategory() != 'Admin' and insertProjectID not in uPackets:
e = InsertProjectAccessException("You are not authorized to use this Insert, since you do not have Read access to its project.")
print `e.err_code()`
return
if pvID > 0 and insertID > 0 :
# try to reconstruct sequence and issue warning if unable
if pvSeqID > 0 and insertSeqID > 0:
# fetch insert cloning sites
insertCloningSites = []
fpcs_prop_id = pHandler.findPropID("5' cloning site")
tpcs_prop_id = pHandler.findPropID("3' cloning site")
fp_insert_cs = rHandler.findSimplePropertyValue(insertID, fpcs_prop_id)
tp_insert_cs = rHandler.findSimplePropertyValue(insertID, tpcs_prop_id)
# Determine if this is a Gateway clone from sites
gwSites = False;
if fp_insert_cs and tp_insert_cs and fp_insert_cs.lower() == 'attl' and tp_insert_cs.lower() == 'attl':
gwSites = True
elif not fp_insert_cs or not tp_insert_cs:
gwSites = True
# nov. 16/07: added this for check
elif fp_insert_cs.lower() in gatewaySites or tp_insert_cs.lower() in gatewaySites:
gwSites = True
else:
gwSites = False;
if gwSites:
# this is a gateway clone
# if sites were changed to something other than gateway, clear sequence
if newFivePrime.lower() != 'attl' or newThreePrime.lower() != 'attl':
e = InsertSitesNotFoundOnParentSequenceException()
print `e.err_code()`
return
else:
pvSeqKey = rHandler.findDNASequenceKey(pvID)
# For Gateway clones, linkers are found from primers - so find the sense and antisense Oligos for this Insert
insertLinkers = []
# Find Sense and Antisense Oligos for this Insert
# (not using antisense just yet - verify with Karen)
iHandler = InsertHandler(db, cursor)
senseOligoID = iHandler.findSenseOligoID(insertID)
#antisenseOligoID = iHandler.findAntisenseOligoID(insert_db_id)
# Find Oligo sequences
seqPropID = pHandler.findPropID("sequence")
senseOligoSeqID = rHandler.findIndexPropertyValue(senseOligoID, seqPropID)
senseOligoSequence = dnaHandler.findSequenceByID(senseOligoSeqID)
# Fetch Insert sequence and find linkers from Oligo and Insert sequences
insertSequence = dnaHandler.findSequenceByID(insertSeqID)
attB_const = "ggggacaactttgtacaaaaaagttggc"
fwd_primer_seq = senseOligoSequence[len(attB_const):]
# First, find linkers from Oligos
fwd_linker = dnaHandler.linker_from_oligo(insertSequence, fwd_primer_seq)
#rev_linker = sHandler.linker_from_oligo(insertSequence, rev_primer_seq)
rev_linker = ""
# Now see if the Insert had its own linkers stored and append them to the Oligo linker
fpLinkerPropID = pHandler.findPropID("5' linker")
tpLinkerPropID = pHandler.findPropID("3' linker")
fp_insert_linker = rHandler.findSimplePropertyValue(insertID, fpLinkerPropID)
tp_insert_linker = rHandler.findSimplePropertyValue(insertID, tpLinkerPropID)
if fp_insert_linker and len(fp_insert_linker) > 0 and fp_insert_linker != 0 and fp_insert_linker != '0':
fp_insert_linker = fwd_linker + fp_insert_linker
else:
fp_insert_linker = fwd_linker
tp_insert_linker = rev_linker
insertLinkers.append(fp_insert_linker)
insertLinkers.append(tp_insert_linker)
try:
newSeq = dnaHandler.entryVectorSequence(pvSeqKey, insertSeqID, insertLinkers)
print newSeq
except MultipleSiteOccurrenceException:
e = MultipleSiteOccurrenceException("Sites found more than once on parent vector sequence")
print `e.err_code()`
except FivePrimeAfterThreePrimeException:
e = FivePrimeAfterThreePrimeException("5' after 3'")
print `e.err_code()`
except InsertSitesNotFoundOnParentSequenceException:
e = InsertSitesNotFoundOnParentSequenceException("Gateway sites not found on parent vector sequence")
print `e.err_code()`
else:
# Non-Gateway non-recombination Vector
fp_insert_cs = newFivePrime
tp_insert_cs = newThreePrime
if fp_insert_cs:
insertCloningSites.append(fp_insert_cs)
else:
insertCloningSites.append("")
if tp_insert_cs:
insertCloningSites.append(tp_insert_cs)
else:
insertCloningSites.append("")
# get linkers if there are any
insertLinkers = []
fpLinkerPropID = pHandler.findPropID("5' linker")
tpLinkerPropID = pHandler.findPropID("3' linker")
fp_insert_linker = rHandler.findSimplePropertyValue(insertID, fpLinkerPropID)
tp_insert_linker = rHandler.findSimplePropertyValue(insertID, tpLinkerPropID)
# sept. 3/07
fwd_linker = ""
if fp_insert_linker and len(fp_insert_linker) > 0 and fp_insert_linker != 0 and fp_insert_linker != '0':
fp_insert_linker = fwd_linker + fp_insert_linker
else:
fp_insert_linker = fwd_linker
insertLinkers.append(fp_insert_linker)
insertLinkers.append(tp_insert_linker)
try:
newSeq = dnaHandler.constructNonRecombSequence(pvSeqID, insertSeqID, insertCloningSites, insertLinkers)
print newSeq
except (InsertSitesException):
e = InsertSitesException("Could not reconstitute sequence: Unknown sites on Insert.")
print e.err_code()
except (InsertSitesNotFoundOnParentSequenceException):
e = InsertSitesNotFoundOnParentSequenceException("Could not reconstitute sequence: Parent vector sequence does not contain restriction sites.")
print e.err_code()
except (MultipleSiteOccurrenceException):
e = MultipleSiteOccurrenceException("Could not reconstitute sequence: Restriction sites occur more than once on parent vector sequence")
print e.err_code()
except (HybridizationException):
e = HybridizationException("Could not reconstitute sequence: Restriction sites cannot be hybridized.")
print e.err_code()
except (FivePrimeAfterThreePrimeException):
e = FivePrimeAfterThreePrimeException("Could not reconstitute sequence: 5' site occurs after 3' site on parent vector sequence.")
print e.err_code()
else:
e = InvalidSequenceException("Invalid parent sequence")
print `e.err_code()`
else:
e = UnknownPVIDException("Unknown PV ID")
print `e.err_code()`
elif cloning_method == '2':
# Recombination vector - check IPV
ipvVal = form.getvalue("IPV")
if len(ipvVal) > 0:
ipvID = rHandler.convertReagentToDatabaseID(ipvVal)
ipvProjectID = int(rHandler.findSimplePropertyValue(ipvID, packetPropID))
else:
e = UnknownIPVIDException("Unknown IPV ID")
print `e.err_code()`
if ipvProjectID > 0 and currUser.getCategory() != 'Admin' and ipvProjectID not in uPackets:
e = IPVProjectAccessException("Not authorized to view IPV")
print `e.err_code()`
if ipvID > 0 and pvID > 0:
# If restriction sites were modified to anything other than LoxP or gateway att sites, clear the sequence
if not (newFivePrime == newThreePrime and (newFivePrime.lower() == 'loxp' and newThreePrime.lower() == 'loxp') or (newFivePrime.lower() == 'attb' and newThreePrime.lower() == 'attb')):
e = InsertSitesNotFoundOnParentSequenceException("Invalid restriction sites for Non-Recombination Clone - must be LoxP only")
print `e.err_code()`
else:
# get internal db IDs
pv_db_id = rHandler.convertReagentToDatabaseID(pvVal)
ipv_db_id = rHandler.convertReagentToDatabaseID(ipvVal)
# Get the Insert that belongs to the donor vector
ipvInsertAssocID = raHandler.findReagentAssociationID(ipv_db_id)
insertAssocPropID = aHandler.findAssocPropID("insert id")
insert_db_id = aHandler.findAssocPropValue(ipvInsertAssocID, insertAssocPropID)
# Construct a sequence for the new vector from the sequences of its parents
pvSeqKey = rHandler.findDNASequenceKey(pv_db_id)
#print "pv seq " + `pvSeqKey`
ipvSeqKey = rHandler.findDNASequenceKey(ipv_db_id)
#print "ipv seq " + `ipvSeqKey`
insertSeqKey = rHandler.findDNASequenceKey(insert_db_id)
#print "i seq " + `insertSeqKey`
if pvSeqKey > 0 and ipvSeqKey > 0 and insertSeqKey > 0:
# See if there are linkers, although there most likely aren't any
insertLinkers = []
fpLinkerPropID = pHandler.findPropID("5' linker")
tpLinkerPropID = pHandler.findPropID("3' linker")
fp_insert_linker = rHandler.findSimplePropertyValue(insert_db_id, fpLinkerPropID)
tp_insert_linker = rHandler.findSimplePropertyValue(insert_db_id, tpLinkerPropID)
# sept. 3/07
fwd_linker = ""
if fp_insert_linker and len(fp_insert_linker) > 0 and fp_insert_linker != 0 and fp_insert_linker != '0':
fp_insert_linker = fwd_linker + fp_insert_linker
else:
fp_insert_linker = fwd_linker
insertLinkers.append(fp_insert_linker)
insertLinkers.append(tp_insert_linker)
# Differentiate by cloning sites whether this is a recombination vector or a Gateway Expression Vector
if newFivePrime == 'LoxP' and newThreePrime == 'LoxP':
# recombination
try:
newSeq = dnaHandler.constructRecombSequence(pvSeqKey, ipvSeqKey, insertSeqKey, insertLinkers)
newSeqID = dnaHandler.matchSequence(newSeq)
print newSeq
except InsertSitesNotFoundOnParentSequenceException:
e = InsertSitesNotFoundOnParentSequenceException("LOXP sites not found on parent vector sequence")
print `e.err_code()`
except MultipleSiteOccurrenceException:
e = MultipleSiteOccurrenceException("LOXP found more than once on parent vector sequence")
print `e.err_code()`
elif newFivePrime == 'attB' and newThreePrime == 'attB':
# Gateway Expression
iHandler = InsertHandler(db, cursor)
senseOligoID = iHandler.findSenseOligoID(insert_db_id)
#antisenseOligoID = iHandler.findAntisenseOligoID(insert_db_id)
# Find Oligo sequences
seqPropID = pHandler.findPropID("sequence")
senseOligoSeqID = rHandler.findIndexPropertyValue(senseOligoID, seqPropID)
senseOligoSequence = dnaHandler.findSequenceByID(senseOligoSeqID)
# Fetch Insert sequence and find linkers from Oligo and Insert sequences
insertSequence = dnaHandler.findSequenceByID(insertSeqKey)
attB_const = "ggggacaactttgtacaaaaaagttggc"
fwd_primer_seq = senseOligoSequence[len(attB_const):]
# First, find linkers from Oligos
fwd_linker = dnaHandler.linker_from_oligo(insertSequence, fwd_primer_seq)
#rev_linker = sHandler.linker_from_oligo(insertSequence, rev_primer_seq)
rev_linker = ""
# Now see if the Insert had its own linkers stored and append them to the Oligo linker
fpLinkerPropID = pHandler.findPropID("5' linker")
tpLinkerPropID = pHandler.findPropID("3' linker")
fp_insert_linker = rHandler.findSimplePropertyValue(insert_db_id, fpLinkerPropID)
tp_insert_linker = rHandler.findSimplePropertyValue(insert_db_id, tpLinkerPropID)
if fp_insert_linker and len(fp_insert_linker) > 0 and fp_insert_linker != 0 and fp_insert_linker != '0':
fp_insert_linker = fwd_linker + fp_insert_linker
else:
fp_insert_linker = fwd_linker
tp_insert_linker = rev_linker
insertLinkers.append(fp_insert_linker)
insertLinkers.append(tp_insert_linker)
try:
newSeq = dnaHandler.expressionVectorSequence(pvSeqKey, insertSeqKey, insertLinkers)
print newSeq
except MultipleSiteOccurrenceException:
e = MultipleSiteOccurrenceException("Sites found more than once on parent vector sequence")
print `e.err_code()`
except FivePrimeAfterThreePrimeException:
e = FivePrimeAfterThreePrimeException("5' after 3'")
print `e.err_code()`
except InsertSitesNotFoundOnParentSequenceException:
e = InsertSitesNotFoundOnParentSequenceException("Gateway sites not found on parent vector sequence")
print `e.err_code()`
else:
e = InvalidSequenceException("Invalid parent sequence")
print `e.err_code()`
else:
e = ReagentDoesNotExistException("Unknown parent values")
print `e.err_code()`
def handle(self):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
mail_server = self.__mail_server # August 19, 2011
mail_admin = self.__mail_admin # August 19, 2011
clone_request = self.__clone_request
form = cgi.FieldStorage(keep_blank_values="True")
uHandler = UserHandler(db, cursor)
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
if form.has_key("curr_username"):
# store the user ID for use throughout the session; add to other views in addition to create in PHP
currUname = form.getvalue("curr_username")
currUser = uHandler.getUserByDescription(currUname)
Session.setUser(currUser)
elif form.has_key("curr_user_id"):
currUID = form.getvalue("curr_user_id")
currUser = uHandler.getUserByID(currUID)
Session.setUser(currUser)
if form.has_key("add_user"):
self.addUser(form)
elif form.has_key("modify_user"):
self.modifyUser(form)
elif form.has_key("cancel_user"):
self.cancelUserModification(form)
elif form.has_key("save_user"):
self.saveUser(form)
elif form.has_key("delete_user"):
self.deleteUser(form)
elif form.has_key("view_user") and form.getvalue(
"view_user") != "" and not form.has_key(
"modify_lab") and not form.has_key("delete_lab"):
self.viewUser(form)
# Nov. 17/07 - Personal user page
elif form.has_key("view_user") and form.getvalue(
"view_user") == "" and not form.has_key(
"modify_lab") and not form.has_key("delete_lab"):
self.printUserInfo('view', currUser)
elif form.has_key("add_lab"):
self.addLab(form)
elif form.has_key("view_lab"):
self.viewLab(form)
elif form.has_key("modify_lab"):
self.modifyLab(form)
elif form.has_key("save_lab"):
self.saveLab(form)
elif form.has_key("cancel_lab"):
self.cancelLabModification(form)
elif form.has_key("delete_lab"):
self.deleteLab(form)
elif form.has_key("bug_report"):
self.submitBug(form)
elif form.has_key("send_order"):
######################################################################
# CHANGE SERVER NAME AND EMAIL TO YOUR LOCAL CREDENTIALS
######################################################################
userID = form.getvalue("curr_user_id")
userDescr = form.getvalue("curr_username")
from_email = uHandler.findEmail(userID)
if not from_email:
from_email = userDescr
to_email = clone_request
email_subject = userDescr + ": Clone Request"
f_in = form.getvalue("outputContent")
infile = open(f_in, 'rb')
msg = email.MIMEMultipart.MIMEMultipart()
#msg.attach(email.MIMEText.MIMEText(infile.read())) # no, this attaches plain text
msg['Subject'] = email_subject
part = email.MIMEBase.MIMEBase('application', "octet-stream")
part.set_payload(infile.read())
email.Utils.base64.standard_b64encode(infile.read())
part.add_header(
'Content-Disposition',
'attachment; filename="%s"' % os.path.basename(f_in))
msg.attach(part)
server = smtplib.SMTP(mail_server)
server.set_debuglevel(1)
# Send a request to your clone request address
server.sendmail(from_email, to_email, msg.as_string())
# AND send a copy to the user (change the subject)
#msg['Subject'] = "Clone request confirmation" # doesn't change, investigate later
# Return email text changed March 31/08
#######################################
# CHANGE TEXT AS NEEDED
#######################################
msg.attach(
email.MIMEText.MIMEText(
"This is a copy of your clone request. Please retain for your records. You will be notified by e-mail when your clone is ready."
))
server.sendmail(to_email, from_email, msg.as_string())
server.quit()
# Method 2
#sendmail = "/usr/sbin/sendmail"
#o = os.popen("%s -t" % sendmail,"w")
#o.write("To: %s\r\n" % to_email)
#if from_email:
#o.write("From: %s\r\n" % from_email)
#o.write("Subject: %s\r\n" % email_subject)
#o.write("\r\n")
#o.write("%s\r\n" % msg)
#o.close()
os.remove(f_in) # delete the file from /tmp dir
utils.redirect(hostname + "User.php?View=8&Sent=1")
# June 1, 2010: Automated password reset
elif form.has_key("reset_pw"):
# change June 2, 2010: Don't enter email, rather, ask users to enter their username - more secure
#to_email = form.getvalue("email")
from_email = mail_admin
#success = True
chars = string.letters + string.digits
new_passwd = ""
for i in range(10):
new_passwd += choice(chars)
# reset it in the database
if form.has_key("uName"):
u_name = form.getvalue("uName")
userID = uHandler.findUserIDByUsername(u_name)
if userID > 0:
u_descr = uHandler.findDescription(userID)
to_email = uHandler.findEmail(userID)
uHandler.setUserPropertyValue(userID, 'password',
new_passwd)
email_subject = "OpenFreezer Password Change"
msg = email.MIMEMultipart.MIMEMultipart()
#msg.attach(email.MIMEText.MIMEText(infile.read())) # no, this attaches plain text
msg['Subject'] = email_subject
###################################
# CHANGE TEXT AS NEEDED
###################################
msg.attach(
email.MIMEText.MIMEText(
"Dear " + u_descr +
",\n\nYour password for OpenFreezer has been changed.\n\nYour temporary new password is: "
+ new_passwd +
".\n\nPlease change the temporary password as soon as you log into the system.\n\nYour username for OpenFreezer is '"
+ u_name +
"'.\n\nFor any questions, please refer to http://openfreezer.org. \n\nSincerely,\nOpenFreezer support team.\n--------------------------------\nThis is an automatically generated e-mail message. Please do not reply to this e-mail. All questions should be directed to your local administrator."
))
server = smtplib.SMTP(mail_server)
server.set_debuglevel(1)
server.sendmail(from_email, to_email, msg.as_string())
server.quit()
utils.redirect(hostname + "User.php?View=6&Reset=1&uid=" +
` userID `)
else:
# retry by description
if form.has_key("uDesc"):
u_descr = form.getvalue("uDesc")
# but account for whitespace
toks = u_descr.split(" ")
tmp_descr = ""
for tok in toks:
tmp_descr += tok.strip() + " "
# strip extra whitespace from end
tmp_descr = tmp_descr.strip()
userID = uHandler.findUserIDByDescription(tmp_descr)
if userID > 0:
u_name = uHandler.findUsername(userID)
to_email = uHandler.findEmail(userID)
uHandler.setUserPropertyValue(
userID, 'password', new_passwd)
email_subject = "OpenFreezer Password Change"
msg = email.MIMEMultipart.MIMEMultipart()
#msg.attach(email.MIMEText.MIMEText(infile.read())) # no, this attaches plain text
msg['Subject'] = email_subject
##############################
# CHANGE TEXT AS NEEDED
##############################
msg.attach(
email.MIMEText.MIMEText(
"Dear " + u_descr +
",\n\nYour password for OpenFreezer has been changed.\n\nYour temporary new password is: "
+ new_passwd +
".\n\nPlease change the temporary password as soon as you log into the system.\n\nYour username for OpenFreezer is '"
+ u_name +
"'.\n\nPlease refer to http://openfreezer.org for additional support.\n\nSincerely,\nOpenFreezer support team.\n--------------------------------\nThis is an automatically generated e-mail message. Please do not reply to this e-mail. All questions should be directed to <a href='mailto:"
+ mail_admin + "'>" + mail_admin + "</a>"))
server = smtplib.SMTP(mail_server)
server.set_debuglevel(1)
server.sendmail(from_email, to_email,
msg.as_string())
server.quit()
utils.redirect(hostname +
"User.php?View=6&Reset=1&uid=" +
` userID `)
else:
utils.redirect(hostname +
"User.php?View=6&Reset=0")
else:
utils.redirect(hostname + "User.php?View=6&Reset=0")
else:
utils.redirect(hostname + "User.php?View=6&Reset=0")
cursor.close()
db.close()
def update():
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
form = cgi.FieldStorage(keep_blank_values="True")
print "Content-type:text/html" # REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
print # DITTO
#print `form`
# Aug 29/07
uHandler = UserHandler(db, cursor)
if form.has_key("curr_username"):
# store the user ID for use throughout the session; add to other views in addition to create in PHP
currUname = form.getvalue("curr_username")
currUser = uHandler.getUserByDescription(currUname)
Session.setUser(currUser)
#else: # debug
#currUname = 'Administrator'
#currUser = uHandler.getUserByDescription(currUname)
#Session.setUser(currUser)
if form.has_key("cloning_method"):
cloning_method = form.getvalue("cloning_method")
#else: # debug
#cloning_method = '1'
# Handlers and mappers
rHandler = ReagentHandler(db, cursor)
#sHandler = SystemSetHandler(db, cursor)
pHandler = ReagentPropertyHandler(db, cursor)
raHandler = ReagentAssociationHandler(db, cursor)
aHandler = AssociationHandler(db, cursor)
dnaHandler = DNAHandler(db, cursor)
commHandler = CommentHandler(db, cursor)
protHandler = ProteinHandler(db, cursor)
propMapper = ReagentPropertyMapper(db, cursor)
assocMapper = ReagentAssociationMapper(db, cursor)
# August 29/07: Restrict creation by user and project access
packetHandler = ProjectDatabaseHandler(db, cursor)
########################################################
# Various maps
########################################################
prop_Alias_ID_Map = propMapper.mapPropAliasID(
) # (propAlias, propID) - e.g. ('insert_type', '48') --> represents 'type of insert' property
prop_Name_Alias_Map = propMapper.mapPropNameAlias(
) # (propName, propAlias)
prop_Name_ID_Map = propMapper.mapPropNameID() # (prop name, prop id)
# Restriction sites
fpcs_prop_id = pHandler.findPropID("5' cloning site")
tpcs_prop_id = pHandler.findPropID("3' cloning site")
newFivePrime = form.getvalue("fpcs")
newThreePrime = form.getvalue("tpcs")
gatewaySites = ['attb', 'attl', 'attp', 'attr'] # nov. 16/07
# resulting sequence
newSeq = ""
# Fetch projects the user has AT LEAST Read access to (i.e. if he is explicitly declared a Writer on a project but not declared a Reader, include that project, plus all public projects)
currReadProj = packetHandler.findMemberProjects(currUser.getUserID(),
'Reader')
currWriteProj = packetHandler.findMemberProjects(currUser.getUserID(),
'Writer')
publicProj = packetHandler.findAllProjects(isPrivate="FALSE")
# list of Packet OBJECTS
currUserWriteProjects = utils.unique(currReadProj + currWriteProj +
publicProj)
uPackets = []
for p in currUserWriteProjects:
uPackets.append(p.getNumber())
# Get project IDs of parents
packetPropID = pHandler.findPropID("packet id")
# August 29/07: Need to verify parent project access AND (Sept. 12/07) reconstruct the sequence IFF parent values are changed
newSeq = ""
# Fetch projects the user has AT LEAST Read access to (i.e. if he is explicitly declared a Writer on a project but not declared a Reader, include that project, plus all public projects)
currReadProj = packetHandler.findMemberProjects(currUser.getUserID(),
'Reader')
currWriteProj = packetHandler.findMemberProjects(currUser.getUserID(),
'Writer')
publicProj = packetHandler.findAllProjects(isPrivate="FALSE")
# list of Packet OBJECTS
currUserWriteProjects = utils.unique(currReadProj + currWriteProj +
publicProj)
uPackets = []
for p in currUserWriteProjects:
uPackets.append(p.getNumber())
# Get project IDs of parents
packetPropID = pHandler.findPropID("packet id")
if form.has_key("PV"):
pvVal = form.getvalue("PV")
if len(pvVal) > 0:
pvID = rHandler.convertReagentToDatabaseID(pvVal)
try:
pvProjectID = int(
rHandler.findSimplePropertyValue(pvID, packetPropID))
pvSeqID = rHandler.findDNASequenceKey(
pvID) # get sequence for reconstitution later
except TypeError:
#pvProjectID = 0
e = PVProjectAccessException(
"You are not authorized to use this Parent Vector, since you do not have Read access to its project."
)
print ` e.err_code() `
else:
e = UnknownPVIDException("Unknown Parent Vector value")
print ` e.err_code() `
return
# else don't do anything, maybe want to delete parents!!!
#else:
#e = MissingPVException("No Parent Vector provided")
#print `e.err_code()`
if pvProjectID > 0 and currUser.getCategory(
) != 'Admin' and pvProjectID not in uPackets:
e = PVProjectAccessException("Not authorized to access parent")
print ` e.err_code() `
return
if cloning_method == '1':
# Non-recombination vector - Get the Insert
if form.has_key("I"):
insertVal = form.getvalue("I")
if len(insertVal) > 0:
insertID = rHandler.convertReagentToDatabaseID(insertVal)
insertSeqID = rHandler.findDNASequenceKey(
insertID) # fetch Insert sequence for reconstitution later
try:
insertProjectID = int(
rHandler.findSimplePropertyValue(
insertID, packetPropID))
except TypeError:
#insertProjectID = 0
e = InsertProjectAccessException(
"You are not authorized to use this Insert, since you do not have Read access to its project."
)
print ` e.err_code() `
else:
#insertID = -1
#insertProjectID = 0
#print "Invalid Insert value"
e = UnknownInsertIDException("Unknown Insert value")
print ` e.err_code() `
return
#else: # NO!!!!!!!!
#e = MissingInsertException("No Insert provided")
#print `e.err_code()`
if insertProjectID > 0 and currUser.getCategory(
) != 'Admin' and insertProjectID not in uPackets:
e = InsertProjectAccessException(
"You are not authorized to use this Insert, since you do not have Read access to its project."
)
print ` e.err_code() `
return
if pvID > 0 and insertID > 0:
# try to reconstruct sequence and issue warning if unable
if pvSeqID > 0 and insertSeqID > 0:
# fetch insert cloning sites
insertCloningSites = []
fpcs_prop_id = pHandler.findPropID("5' cloning site")
tpcs_prop_id = pHandler.findPropID("3' cloning site")
fp_insert_cs = rHandler.findSimplePropertyValue(
insertID, fpcs_prop_id)
tp_insert_cs = rHandler.findSimplePropertyValue(
insertID, tpcs_prop_id)
# Determine if this is a Gateway clone from sites
gwSites = False
if fp_insert_cs and tp_insert_cs and fp_insert_cs.lower(
) == 'attl' and tp_insert_cs.lower() == 'attl':
gwSites = True
elif not fp_insert_cs or not tp_insert_cs:
gwSites = True
# nov. 16/07: added this for check
elif fp_insert_cs.lower(
) in gatewaySites or tp_insert_cs.lower() in gatewaySites:
gwSites = True
else:
gwSites = False
if gwSites:
# this is a gateway clone
# if sites were changed to something other than gateway, clear sequence
if newFivePrime.lower() != 'attl' or newThreePrime.lower(
) != 'attl':
e = InsertSitesNotFoundOnParentSequenceException()
print ` e.err_code() `
return
else:
pvSeqKey = rHandler.findDNASequenceKey(pvID)
# For Gateway clones, linkers are found from primers - so find the sense and antisense Oligos for this Insert
insertLinkers = []
# Find Sense and Antisense Oligos for this Insert
# (not using antisense just yet - verify with Karen)
iHandler = InsertHandler(db, cursor)
senseOligoID = iHandler.findSenseOligoID(insertID)
#antisenseOligoID = iHandler.findAntisenseOligoID(insert_db_id)
# Find Oligo sequences
seqPropID = pHandler.findPropID("sequence")
senseOligoSeqID = rHandler.findIndexPropertyValue(
senseOligoID, seqPropID)
senseOligoSequence = dnaHandler.findSequenceByID(
senseOligoSeqID)
# Fetch Insert sequence and find linkers from Oligo and Insert sequences
insertSequence = dnaHandler.findSequenceByID(
insertSeqID)
attB_const = "ggggacaactttgtacaaaaaagttggc"
fwd_primer_seq = senseOligoSequence[len(attB_const):]
# First, find linkers from Oligos
fwd_linker = dnaHandler.linker_from_oligo(
insertSequence, fwd_primer_seq)
#rev_linker = sHandler.linker_from_oligo(insertSequence, rev_primer_seq)
rev_linker = ""
# Now see if the Insert had its own linkers stored and append them to the Oligo linker
fpLinkerPropID = pHandler.findPropID("5' linker")
tpLinkerPropID = pHandler.findPropID("3' linker")
fp_insert_linker = rHandler.findSimplePropertyValue(
insertID, fpLinkerPropID)
tp_insert_linker = rHandler.findSimplePropertyValue(
insertID, tpLinkerPropID)
if fp_insert_linker and len(
fp_insert_linker
) > 0 and fp_insert_linker != 0 and fp_insert_linker != '0':
fp_insert_linker = fwd_linker + fp_insert_linker
else:
fp_insert_linker = fwd_linker
tp_insert_linker = rev_linker
insertLinkers.append(fp_insert_linker)
insertLinkers.append(tp_insert_linker)
try:
newSeq = dnaHandler.entryVectorSequence(
pvSeqKey, insertSeqID, insertLinkers)
print newSeq
except MultipleSiteOccurrenceException:
e = MultipleSiteOccurrenceException(
"Sites found more than once on parent vector sequence"
)
print ` e.err_code() `
except FivePrimeAfterThreePrimeException:
e = FivePrimeAfterThreePrimeException(
"5' after 3'")
print ` e.err_code() `
except InsertSitesNotFoundOnParentSequenceException:
e = InsertSitesNotFoundOnParentSequenceException(
"Gateway sites not found on parent vector sequence"
)
print ` e.err_code() `
else:
# Non-Gateway non-recombination Vector
fp_insert_cs = newFivePrime
tp_insert_cs = newThreePrime
if fp_insert_cs:
insertCloningSites.append(fp_insert_cs)
else:
insertCloningSites.append("")
if tp_insert_cs:
insertCloningSites.append(tp_insert_cs)
else:
insertCloningSites.append("")
# get linkers if there are any
insertLinkers = []
fpLinkerPropID = pHandler.findPropID("5' linker")
tpLinkerPropID = pHandler.findPropID("3' linker")
fp_insert_linker = rHandler.findSimplePropertyValue(
insertID, fpLinkerPropID)
tp_insert_linker = rHandler.findSimplePropertyValue(
insertID, tpLinkerPropID)
# sept. 3/07
fwd_linker = ""
if fp_insert_linker and len(
fp_insert_linker
) > 0 and fp_insert_linker != 0 and fp_insert_linker != '0':
fp_insert_linker = fwd_linker + fp_insert_linker
else:
fp_insert_linker = fwd_linker
insertLinkers.append(fp_insert_linker)
insertLinkers.append(tp_insert_linker)
try:
newSeq = dnaHandler.constructNonRecombSequence(
pvSeqID, insertSeqID, insertCloningSites,
insertLinkers)
print newSeq
except (InsertSitesException):
e = InsertSitesException(
"Could not reconstitute sequence: Unknown sites on Insert."
)
print e.err_code()
except (InsertSitesNotFoundOnParentSequenceException):
e = InsertSitesNotFoundOnParentSequenceException(
"Could not reconstitute sequence: Parent vector sequence does not contain restriction sites."
)
print e.err_code()
except (MultipleSiteOccurrenceException):
e = MultipleSiteOccurrenceException(
"Could not reconstitute sequence: Restriction sites occur more than once on parent vector sequence"
)
print e.err_code()
except (HybridizationException):
e = HybridizationException(
"Could not reconstitute sequence: Restriction sites cannot be hybridized."
)
print e.err_code()
except (FivePrimeAfterThreePrimeException):
e = FivePrimeAfterThreePrimeException(
"Could not reconstitute sequence: 5' site occurs after 3' site on parent vector sequence."
)
print e.err_code()
else:
e = InvalidSequenceException("Invalid parent sequence")
print ` e.err_code() `
else:
e = UnknownPVIDException("Unknown PV ID")
print ` e.err_code() `
elif cloning_method == '2':
# Recombination vector - check IPV
ipvVal = form.getvalue("IPV")
if len(ipvVal) > 0:
ipvID = rHandler.convertReagentToDatabaseID(ipvVal)
ipvProjectID = int(
rHandler.findSimplePropertyValue(ipvID, packetPropID))
else:
e = UnknownIPVIDException("Unknown IPV ID")
print ` e.err_code() `
if ipvProjectID > 0 and currUser.getCategory(
) != 'Admin' and ipvProjectID not in uPackets:
e = IPVProjectAccessException("Not authorized to view IPV")
print ` e.err_code() `
if ipvID > 0 and pvID > 0:
# If restriction sites were modified to anything other than LoxP or gateway att sites, clear the sequence
if not (newFivePrime == newThreePrime and
(newFivePrime.lower() == 'loxp'
and newThreePrime.lower() == 'loxp') or
(newFivePrime.lower() == 'attb'
and newThreePrime.lower() == 'attb')):
e = InsertSitesNotFoundOnParentSequenceException(
"Invalid restriction sites for Non-Recombination Clone - must be LoxP only"
)
print ` e.err_code() `
else:
# get internal db IDs
pv_db_id = rHandler.convertReagentToDatabaseID(pvVal)
ipv_db_id = rHandler.convertReagentToDatabaseID(ipvVal)
# Get the Insert that belongs to the donor vector
ipvInsertAssocID = raHandler.findReagentAssociationID(
ipv_db_id)
insertAssocPropID = aHandler.findAssocPropID("insert id")
insert_db_id = aHandler.findAssocPropValue(
ipvInsertAssocID, insertAssocPropID)
# Construct a sequence for the new vector from the sequences of its parents
pvSeqKey = rHandler.findDNASequenceKey(pv_db_id)
#print "pv seq " + `pvSeqKey`
ipvSeqKey = rHandler.findDNASequenceKey(ipv_db_id)
#print "ipv seq " + `ipvSeqKey`
insertSeqKey = rHandler.findDNASequenceKey(insert_db_id)
#print "i seq " + `insertSeqKey`
if pvSeqKey > 0 and ipvSeqKey > 0 and insertSeqKey > 0:
# See if there are linkers, although there most likely aren't any
insertLinkers = []
fpLinkerPropID = pHandler.findPropID("5' linker")
tpLinkerPropID = pHandler.findPropID("3' linker")
fp_insert_linker = rHandler.findSimplePropertyValue(
insert_db_id, fpLinkerPropID)
tp_insert_linker = rHandler.findSimplePropertyValue(
insert_db_id, tpLinkerPropID)
# sept. 3/07
fwd_linker = ""
if fp_insert_linker and len(
fp_insert_linker
) > 0 and fp_insert_linker != 0 and fp_insert_linker != '0':
fp_insert_linker = fwd_linker + fp_insert_linker
else:
fp_insert_linker = fwd_linker
insertLinkers.append(fp_insert_linker)
insertLinkers.append(tp_insert_linker)
# Differentiate by cloning sites whether this is a recombination vector or a Gateway Expression Vector
if newFivePrime == 'LoxP' and newThreePrime == 'LoxP':
# recombination
try:
newSeq = dnaHandler.constructRecombSequence(
pvSeqKey, ipvSeqKey, insertSeqKey,
insertLinkers)
newSeqID = dnaHandler.matchSequence(newSeq)
print newSeq
except InsertSitesNotFoundOnParentSequenceException:
e = InsertSitesNotFoundOnParentSequenceException(
"LOXP sites not found on parent vector sequence"
)
print ` e.err_code() `
except MultipleSiteOccurrenceException:
e = MultipleSiteOccurrenceException(
"LOXP found more than once on parent vector sequence"
)
print ` e.err_code() `
elif newFivePrime == 'attB' and newThreePrime == 'attB':
# Gateway Expression
iHandler = InsertHandler(db, cursor)
senseOligoID = iHandler.findSenseOligoID(insert_db_id)
#antisenseOligoID = iHandler.findAntisenseOligoID(insert_db_id)
# Find Oligo sequences
seqPropID = pHandler.findPropID("sequence")
senseOligoSeqID = rHandler.findIndexPropertyValue(
senseOligoID, seqPropID)
senseOligoSequence = dnaHandler.findSequenceByID(
senseOligoSeqID)
# Fetch Insert sequence and find linkers from Oligo and Insert sequences
insertSequence = dnaHandler.findSequenceByID(
insertSeqKey)
attB_const = "ggggacaactttgtacaaaaaagttggc"
fwd_primer_seq = senseOligoSequence[len(attB_const):]
# First, find linkers from Oligos
fwd_linker = dnaHandler.linker_from_oligo(
insertSequence, fwd_primer_seq)
#rev_linker = sHandler.linker_from_oligo(insertSequence, rev_primer_seq)
rev_linker = ""
# Now see if the Insert had its own linkers stored and append them to the Oligo linker
fpLinkerPropID = pHandler.findPropID("5' linker")
tpLinkerPropID = pHandler.findPropID("3' linker")
fp_insert_linker = rHandler.findSimplePropertyValue(
insert_db_id, fpLinkerPropID)
tp_insert_linker = rHandler.findSimplePropertyValue(
insert_db_id, tpLinkerPropID)
if fp_insert_linker and len(
fp_insert_linker
) > 0 and fp_insert_linker != 0 and fp_insert_linker != '0':
fp_insert_linker = fwd_linker + fp_insert_linker
else:
fp_insert_linker = fwd_linker
tp_insert_linker = rev_linker
insertLinkers.append(fp_insert_linker)
insertLinkers.append(tp_insert_linker)
try:
newSeq = dnaHandler.expressionVectorSequence(
pvSeqKey, insertSeqKey, insertLinkers)
print newSeq
except MultipleSiteOccurrenceException:
e = MultipleSiteOccurrenceException(
"Sites found more than once on parent vector sequence"
)
print ` e.err_code() `
except FivePrimeAfterThreePrimeException:
e = FivePrimeAfterThreePrimeException(
"5' after 3'")
print ` e.err_code() `
except InsertSitesNotFoundOnParentSequenceException:
e = InsertSitesNotFoundOnParentSequenceException(
"Gateway sites not found on parent vector sequence"
)
print ` e.err_code() `
else:
e = InvalidSequenceException("Invalid parent sequence")
print ` e.err_code() `
else:
e = ReagentDoesNotExistException("Unknown parent values")
print ` e.err_code() `
