def createProject(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
# Handlers
pHandler = ProjectDatabaseHandler(db, cursor)
uHandler = UserHandler(db, cursor)
# Get form values
projectID = form.getvalue("packetID")
ownerID = form.getvalue("packetOwner")
# get owner's name
packetOwner = uHandler.getUserByID(ownerID)
packetName = form.getvalue("packetName")
packetDescription = form.getvalue("packetDescription")
# private or public
if form.getvalue("private_or_public") == "public":
isPrivate = False
else:
isPrivate = True
# Lists of project readers & editors
# These are lists of INTEGER USER IDs!!!!!
# A User instance needs to be created for each!!!!!!!
projectReaderIDs = form.getlist("readersTargetList")
projectWriterIDs = form.getlist("writersTargetList")
projectReaders = []
projectWriters = []
for rID in projectReaderIDs:
tmpReader = uHandler.getUserByID(rID)
projectReaders.append(tmpReader)
for wID in projectWriterIDs:
tmpWriter = uHandler.getUserByID(wID)
# Now check if the user is an OpenFreezer writer - otherwise cannot be made Writer on a project
if tmpWriter.getCategory() != 'Reader':
projectWriters.append(tmpWriter)
newProject = Packet(projectID, packetName, packetDescription,
packetOwner, isPrivate, projectReaders,
projectWriters)
packetID = pHandler.insertPacket(
newProject) # new project is empty by default
self.showProjectDetails('view', newProject)
def createProject(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
# Handlers
pHandler = ProjectDatabaseHandler(db, cursor)
uHandler = UserHandler(db, cursor)
# Get form values
projectID = form.getvalue("packetID")
ownerID = form.getvalue("packetOwner")
# get owner's name
packetOwner = uHandler.getUserByID(ownerID)
packetName = form.getvalue("packetName")
packetDescription = form.getvalue("packetDescription")
# private or public
if form.getvalue("private_or_public") == "public":
isPrivate = False
else:
isPrivate = True
# Lists of project readers & editors
# These are lists of INTEGER USER IDs!!!!!
# A User instance needs to be created for each!!!!!!!
projectReaderIDs = form.getlist("readersTargetList")
projectWriterIDs = form.getlist("writersTargetList")
projectReaders = []
projectWriters = []
for rID in projectReaderIDs:
tmpReader = uHandler.getUserByID(rID)
projectReaders.append(tmpReader)
for wID in projectWriterIDs:
tmpWriter = uHandler.getUserByID(wID)
# Now check if the user is an OpenFreezer writer - otherwise cannot be made Writer on a project
if tmpWriter.getCategory() != 'Reader':
projectWriters.append(tmpWriter)
newProject = Packet(projectID, packetName, packetDescription, packetOwner, isPrivate, projectReaders, projectWriters)
packetID = pHandler.insertPacket(newProject) # new project is empty by default
self.showProjectDetails('view', newProject)
def deleteProject(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
pHandler = ProjectDatabaseHandler(db, cursor)
# Get form values
pID = int(form.getvalue("packetID"))
success = int(pHandler.deleteProject(pID))
utils.redirect(hostname + "Project.php?View=3&Success=" + `success` + "&pID=" + `pID`)
def printProjectInfo(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
projectID = int(form.getvalue('packets'))
pHandler = ProjectDatabaseHandler(db, cursor)
newProject = pHandler.findPacket(projectID)
self.showProjectDetails('view', newProject)
def printProjectInfo(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
projectID = int(form.getvalue('packets'))
pHandler = ProjectDatabaseHandler(db, cursor)
newProject = pHandler.findPacket(projectID)
self.showProjectDetails('view', newProject)
def deleteProject(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
pHandler = ProjectDatabaseHandler(db, cursor)
# Get form values
pID = int(form.getvalue("packetID"))
success = int(pHandler.deleteProject(pID))
utils.redirect(hostname + "Project.php?View=3&Success=" + ` success ` +
"&pID=" + ` pID `)
def modifyProject(self, form):
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
# Handlers
pHandler = ProjectDatabaseHandler(db, cursor)
uHandler = UserHandler(db, cursor)
# Get project ID from form
projectID = form.getvalue("packetID")
ownerID = form.getvalue("packetOwner")
# get owner's name
packetOwner = uHandler.getUserByID(ownerID)
packetName = form.getvalue("packetName")
packetDescription = form.getvalue("packetDescription")
# access type:
accessType = form.getvalue("private_or_public")
if accessType == 'Private':
isPrivate = True
else:
isPrivate = False
# Lists of project readers & editors
# In this view, these are list of INTEGER USER IDs
# A User instance needs to be created for each!!!!!!!
projectReaderIDs = form.getlist("projectReaders")
projectWriterIDs = form.getlist("projectWriters")
projectReaders = []
projectWriters = []
for rID in projectReaderIDs:
tmpReader = uHandler.getUserByID(rID)
projectReaders.append(tmpReader)
for wID in projectWriterIDs:
tmpWriter = uHandler.getUserByID(wID)
projectWriters.append(tmpWriter)
newProject = Packet(projectID, packetName, packetDescription,
packetOwner, isPrivate, projectReaders,
projectWriters)
self.showProjectDetails('edit', newProject)
def modifyUser(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
uHandler = UserHandler(db, cursor)
lHandler = LabHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
ucMapper = UserCategoryMapper(db, cursor)
category_Name_ID_Map = ucMapper.mapCategoryNameToID()
# print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
# print # DITTO
# print `form`
# Get form values
userID = int(form.getvalue("userID"))
newUser = uHandler.getUserByID(userID)
"""
labID = int(form.getvalue("labID"))
username = form.getvalue("username")
firstName = form.getvalue("firstName")
lastName = form.getvalue("lastName")
description = firstName + " " + lastName
email = form.getvalue("email")
passwd = form.getvalue("password")
"""
readProjects = pHandler.findMemberProjects(userID, "Reader")
newUser.setReadProjects(readProjects)
writeProjects = pHandler.findMemberProjects(userID, "Writer")
newUser.setWriteProjects(writeProjects)
self.printUserInfo("edit", newUser)
def modifyUser(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
uHandler = UserHandler(db, cursor)
lHandler = LabHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
ucMapper = UserCategoryMapper(db, cursor)
category_Name_ID_Map = ucMapper.mapCategoryNameToID()
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
# Get form values
userID = int(form.getvalue("userID"))
newUser = uHandler.getUserByID(userID)
'''
labID = int(form.getvalue("labID"))
username = form.getvalue("username")
firstName = form.getvalue("firstName")
lastName = form.getvalue("lastName")
description = firstName + " " + lastName
email = form.getvalue("email")
passwd = form.getvalue("password")
'''
readProjects = pHandler.findMemberProjects(userID, 'Reader')
newUser.setReadProjects(readProjects)
writeProjects = pHandler.findMemberProjects(userID, 'Writer')
newUser.setWriteProjects(writeProjects)
self.printUserInfo('edit', newUser)
def findPacket(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
pHandler = ProjectDatabaseHandler(db, cursor)
packets = []
pString = ""
keyword = form.getvalue("keyword")
packetsList = pHandler.matchProjectKeyword(keyword)
for pID in packetsList:
pText = packetsList[pID]
packets.append(pText)
pString = string.join(packets, ", ")
print "Content-type:text/html"
print
print pString
def findPacket(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
pHandler = ProjectDatabaseHandler(db, cursor)
packets = []
pString = ""
keyword = form.getvalue("keyword")
packetsList = pHandler.matchProjectKeyword(keyword)
for pID in packetsList:
pText = packetsList[pID]
packets.append(pText)
pString = string.join(packets, ", ")
print "Content-type:text/html"
print
print pString
def deleteUser(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
uHandler = UserHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
# print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
# print # DITTO
# print `form`
uid = form.getvalue("userID")
# list of user IDs
# deletionCandidates = form.getlist("deletionCandidates")
# Delete users and revoke their access to projects
# for uid in deletionCandidates:
uHandler.deleteUser(uid)
pHandler.deleteMemberFromllProjects(uid)
utils.redirect(hostname + "User.php?View=2&Del=1")
def deleteUser(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
uHandler = UserHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
uid = form.getvalue("userID")
# list of user IDs
#deletionCandidates = form.getlist("deletionCandidates")
# Delete users and revoke their access to projects
#for uid in deletionCandidates:
uHandler.deleteUser(uid)
pHandler.deleteMemberFromllProjects(uid)
utils.redirect(hostname + "User.php?View=2&Del=1")
def cancelUserModification(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
uHandler = UserHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
userID = int(form.getvalue('userID'))
newUser = uHandler.getUserByID(userID)
self.printUserInfo('view', newUser)
def saveUser(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
# print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
# print # DITTO
# print `form`
uHandler = UserHandler(db, cursor)
lHandler = LabHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
ucMapper = UserCategoryMapper(db, cursor)
category_ID_Name_Map = ucMapper.mapCategoryIDToName()
newProps = {}
# Get form values
userID = int(form.getvalue("userID"))
newUser = uHandler.getUserByID(userID)
labID = int(form.getvalue("labs"))
tmpLab = lHandler.findLabByID(labID)
# rest of user properties
username = form.getvalue("username")
firstName = form.getvalue("firstName")
lastName = form.getvalue("lastName")
description = firstName + " " + lastName
email = form.getvalue("email")
category = category_ID_Name_Map[int(form.getvalue("system_access_level"))]
newProps["labID"] = labID
newProps["username"] = username
newProps["firstname"] = firstName
newProps["lastname"] = lastName
newProps["description"] = description
newProps["email"] = email
newProps["category"] = category
try:
# Now do an update on database level AND on class level:
uHandler.updateUserProperties(userID, newProps) # database update
# Interface level
newUser.setUsername(username)
newUser.setFirstName(firstName)
newUser.setLastName(lastName)
newUser.setDescription(description)
newUser.setEmail(email)
newUser.setLab(tmpLab)
newUser.setCategory(category)
# update list of user's projects
if form.has_key("userProjectsReadonly"):
# list of IDs
readonlyProjects = utils.unique(form.getlist("userProjectsReadonly"))
pHandler.updateUserProjects(userID, readonlyProjects, "Reader")
else:
# safe to assume should delete projects?
pHandler.deleteMemberProjects(userID, "Reader")
if form.has_key("userProjectsWrite"):
writeProjects = utils.unique(form.getlist("userProjectsWrite"))
pHandler.updateUserProjects(userID, writeProjects, "Writer")
else:
# safe to assume should delete projects?
pHandler.deleteMemberProjects(userID, "Writer")
# think about this
# newUser.setReadProjects(readProjects)
# newUser.setWriteProjects(writeProjects)
# return to detailed view
self.printUserInfo("view", newUser)
# utils.redirect(hostname + "User.php?View=3&fd=" + filename)
except DuplicateUsernameException:
# return to the view with input values and error message
# Need to construct a dummy User instance to save form values for error output on the next page (otherwise they're lost as soon as Submit is pressed and creation view is exited)
newLab = lHandler.findLabByID(labID)
newUser = User(userID, username, firstName, lastName, description, newLab, category, email, "")
self.printUserInfo("edit", newUser, "Dup_un")
def saveProject(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
# Handlers
pHandler = ProjectDatabaseHandler(db, cursor)
uHandler = UserHandler(db, cursor)
# Get project ID from form
projectID = form.getvalue("packetID")
ownerID = form.getvalue("packetOwner")
# get owner's name
packetOwner = uHandler.getUserByID(ownerID)
packetName = form.getvalue("packetName")
packetDescription = form.getvalue("packetDescription")
# private or public
if form.getvalue("private_or_public") == "public":
isPrivate = False
else:
isPrivate = True
# Lists of project readers & editors
# Updated Sept. 3/08: Do NOT save readers for a public project
if isPrivate:
projectReaderIDs = form.getlist("readersList")
else:
projectReaderIDs = []
# writers are always needed
projectWriterIDs = form.getlist("writersList")
projectReaders = []
projectWriters = []
for rID in projectReaderIDs:
tmpReader = uHandler.getUserByID(rID)
projectReaders.append(tmpReader)
for wID in projectWriterIDs:
tmpWriter = uHandler.getUserByID(wID)
# check categories - a Reader cannot be given Write access to a project
if tmpWriter.getCategory() != 'Reader':
projectWriters.append(tmpWriter)
#projectWriters.append(tmpWriter)
# Update database values
pHandler.updatePacket(projectID, ownerID, packetName,
packetDescription, isPrivate, projectReaderIDs,
projectWriterIDs)
# Output new values
newProject = Packet(projectID, packetName, packetDescription,
packetOwner, isPrivate, projectReaders,
projectWriters)
self.showProjectDetails('view', newProject)
def addUser(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
mail_server = self.__mail_server # August 19, 2011
mail_programmer = self.__mail_programmer # July 30, 2010
mail_biologist = self.__mail_biologist
mail_admin = self.__mail_admin
# print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
# print # DITTO
# print `form`
uHandler = UserHandler(db, cursor)
lHandler = LabHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
ucMapper = UserCategoryMapper(db, cursor)
category_Name_ID_Map = ucMapper.mapCategoryNameToID()
# Get form values
labID = int(form.getvalue("labs"))
username = form.getvalue("username")
firstName = form.getvalue("firstName")
lastName = form.getvalue("lastName")
description = firstName + " " + lastName
to_email = form.getvalue("email")
from_email = mail_admin
# Change July 30, 2010 - random password generator
# passwd = form.getvalue("password")
chars = string.letters + string.digits
passwd = ""
for i in range(10):
passwd += choice(chars)
# System access level: Lab default or override?
# if form.getvalue("privChoiceRadio") == 'override':
accessLevel = category_Name_ID_Map[form.getvalue("system_access_level")]
# else:
# accessLevel = lHandler.findDefaultAccessLevel(labID)
newProps = {}
try:
# Insert User information
userID = uHandler.insertUser(
username, firstName, lastName, description, accessLevel, to_email, passwd, labID
)
# newUser = uHandler.getUserByID(userID)
tmpLab = lHandler.findLabByID(labID)
# print tmpLab.getName()
# Insert Project info
# Sept. 11/07: Differentiate between user categories Reader and Writer - different field names
if form.has_key("userProjectsReadonly"):
# list of IDs
readonlyProjects = utils.unique(form.getlist("userProjectsReadonly"))
# print `readonlyProjects`
pHandler.insertMemberProjects(userID, readonlyProjects, "Reader")
elif form.has_key("userProjectsReadonlyWrite"):
# list of IDs
readonlyProjects = utils.unique(form.getlist("userProjectsReadonlyWrite"))
# print `readonlyProjects`
pHandler.insertMemberProjects(userID, readonlyProjects, "Reader")
# Write projects exist only for Writers
if form.has_key("userProjectsWrite"):
writeProjects = utils.unique(form.getlist("userProjectsWrite"))
pHandler.insertMemberProjects(userID, writeProjects, "Writer")
# don't assign projects to a User instance - will retrieve them from db in output function
newUser = User(
userID,
username,
firstName,
lastName,
description,
tmpLab,
form.getvalue("system_access_level"),
to_email,
passwd,
[],
[],
)
email_subject = "OpenFreezer User Account"
msg = email.MIMEMultipart.MIMEMultipart("alternative")
msg["Subject"] = email_subject
msg["To"] = to_email
msgText = (
"Hi "
+ firstName
+ ",<BR><BR>An OpenFreezer account has been created for you. Your access level is "
+ form.getvalue("system_access_level")
+ ", so you can "
)
if form.getvalue("system_access_level") == "Reader":
msgText += "search for clones. If you wish to add/modify reagents or create projects, please contact the administrator to upgrade your access level.<BR>"
elif form.getvalue("system_access_level") == "Writer":
msgText += "search, add, and modify reagents. If you wish to create projects, please contact the administrator to upgrade your access level.<BR>"
elif form.getvalue("system_access_level") == "Creator":
msgText += "search for clones, add and modify reagents, as well as create your own projects.<BR>"
#####################################################
# CHANGE TEXT AS NEEDED
#####################################################
msgText += (
"<BR>The URL to access the system is <a href='"
+ hostname
+ "'>"
+ hostname
+ "</a>. Your username is <b>"
+ username
+ "</b>, and your temporary password is <b>"
+ passwd
+ "</b>. Please <u>change the temporary password as soon as you log into the website</u> - you can do it through the 'Change your password' link under the 'User Management' menu section.<BR><BR>Please refer to http://openfreezer.org for additional support.<BR><BR>Sincerely,<BR>OpenFreezer support team.<BR><BR><span style='font-family:Courier; font-size:10pt;'><HR>This is an automatically generated e-mail message. Please do not reply to this e-mail. All questions should be directed to your local administrator.</span>"
)
msgText = email.MIMEText.MIMEText(msgText, "html")
msg.attach(msgText)
server = smtplib.SMTP(mail_server)
server.set_debuglevel(1)
server.sendmail(from_email, [to_email], msg.as_string())
server.quit()
self.printUserInfo("view", newUser)
except DeletedUserException:
# Without asking too many questions, reactivate the deleted user and overwrite his/her attributes with the form input values
userID = uHandler.findUserIDByUsername(username)
newProps["firstname"] = firstName
newProps["lastname"] = lastName
newProps["description"] = description
newProps["email"] = email
newProps["status"] = "ACTIVE"
newProps["password"] = passwd
# Insert new database values and create new object
uHandler.updateUserProperties(userID, newProps) # database update
newUser = uHandler.getUserByID(userID)
# Insert Project info
readProjects = []
writeProjects = []
if form.has_key("userProjectsReadonly"):
# list of IDs
readonlyProjects = form.getlist("userProjectsReadonly")
for r in readonlyProjects:
pHandler.addProjectMember(r, userID, "Reader")
# tmpReadProject = pHandler.findPacket(r)
# readProjects.append(tmpReadProject)
# newUser.addProject(tmpReadProject, 'read')
if form.has_key("userProjectsWrite"):
writeProjects = form.getlist("userProjectsWrite")
for w in writeProjects:
pHandler.addProjectMember(w, userID, "Writer")
# tmpWriteProject = pHandler.findPacket(w)
# writeProjects.append(tmpWriteProject)
# newUser.addProject(tmpWriteProject, 'write')
# newUser.setReadProjects(readProjects)
# newUser.setWriteProjects(writeProjects)
self.printUserInfo("view", newUser)
# utils.redirect(hostname + "User.php?View=3&fd=" + filename)
except DuplicateUsernameException:
# return to the view with input values and error message
# Need to construct a dummy User instance to save form values for error output on the next page (otherwise they're lost as soon as Submit is pressed and creation view is exited)
newLab = lHandler.findLabByID(labID)
newUser = User(0, username, firstName, lastName, description, newLab, "", email, passwd)
self.printUserInfo("create", newUser)
def printReagentInfo(self, cmd, reagent, errMsg=""):
dbConn = DatabaseConn()
hostname = dbConn.getHostname() # to define form action URL
db = dbConn.databaseConnect()
cursor = db.cursor()
gOut = GeneralOutputClass()
currUser = Session.getUser()
currUserID = currUser.getUserID()
sHandler = SystemSetHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
# print menu
content = gOut.printHeader() + gOut.printMainMenu()
# common to all reagent types
projectList = utils.unique(pHandler.findMemberProjects(currUserID, 'Writer') + pHandler.findMemberProjects(currUserID, 'Owner'))
# Differentiate other properties by reagent type
if reagent.getType() == 'Insert':
# Fetch dropdown list values to output on the form
iTypeList = sHandler.findAllSetValues("type of insert")
statusList = sHandler.findAllSetValues("status")
cloningMethodList = sHandler.findAllSetValues("insert cloning method")
fpcsList = sHandler.findAllSetValues("5' cloning site")
tpcsList = sHandler.findAllSetValues("3' cloning site")
tagTypeList = sHandler.findAllSetValues("tag")
tagPositionList = sHandler.findAllSetValues("tag position")
openClosedList = sHandler.findAllSetValues("open/closed")
speciesList = sHandler.findAllSetValues("species")
verificationList = sHandler.findAllSetValues("verification")
# Initialize property values
iType = ""
iName = ""
iStatus = ""
cloningMethod = ""
projectID = ""
fpcs = ""
tpcs = ""
tagType = ""
tagPosition = ""
openClosed = ""
species = ""
accession = ""
altID = ""
geneID = ""
ensemblID = ""
geneSymbol = ""
fp_start = ""
tp_stop = ""
fwd_linker = ""
rev_linker = ""
funcDescr = ""
verification = ""
expComm = ""
verComm = ""
sequence = ""
# Fetch POST values if available:
allProps = reagent.getProperties()
if allProps.has_key("type of insert"):
iType = allProps["type of insert"]
if allProps.has_key("name"):
iName = allProps["name"]
if allProps.has_key("status"):
iStatus = allProps["status"]
if allProps.has_key("insert cloning method"):
cloningMethod = allProps["insert cloning method"]
if allProps.has_key("packet id"):
projectID = int(allProps["packet id"])
if allProps.has_key("5' cloning site"):
fpcs = allProps["5' cloning site"]
if allProps.has_key("3' cloning site"):
tpcs = allProps["3' cloning site"]
if allProps.has_key("tag"):
tagType = allProps["tag"]
if allProps.has_key("tag position"):
tagPosition = allProps["tag position"]
if allProps.has_key("open/closed"):
openClosed = allProps["open/closed"]
if allProps.has_key("species"):
species = allProps["species"]
if allProps.has_key("accession number"):
accession = allProps["accession number"]
if allProps.has_key("alternate id"):
altID = allProps["alternate id"]
if allProps.has_key("entrez gene id"):
geneID = allProps["entrez gene id"]
if allProps.has_key("ensembl gene id"):
ensemblID = allProps["ensembl gene id"]
if allProps.has_key("official gene symbol"):
geneSymbol = allProps["official gene symbol"]
if allProps.has_key("5' start"):
fp_start = allProps["5' start"]
if allProps.has_key("3' stop"):
tp_stop = allProps["3' stop"]
if allProps.has_key("5' linker"):
fwd_linker = allProps["5' linker"]
if allProps.has_key("3' linker"):
rev_linker = allProps["3' linker"]
if allProps.has_key("description"):
funcDescr = allProps["description"]
if allProps.has_key("verification"):
verification = allProps["verification"]
if allProps.has_key("comments"):
expComm = allProps["comments"]
if allProps.has_key("verification comments"):
verComm = allProps["verification comments"]
if allProps.has_key("sequence"):
sequence = allProps["sequence"]
# associations
ipvID = ""
senseOligoID = ""
antisenseOligoID = ""
allAssoc = reagent.getAssociations()
'''
if allAssoc.has_key("insert_parent_vector"):
ipvID = allAssoc["insert_parent_vector"]
if allAssoc.has_key("sense_oligo"):
senseOligoID = allAssoc["sense_oligo"]
if allAssoc.has_key("antisense_oligo"):
antisenseOligoID = allAssoc["antisense_oligo"]
'''
# Action: Output form with POST values if set
if cmd == 'create':
content += '''
<div class="main">
<form NAME="create_insert_form" ACTION="%s" METHOD="POST" onSubmit="return validateInsert() && verifyParents();">
'''
content += "<INPUT type=\"hidden\" ID=\"curr_username_hidden\" NAME=\"curr_username\" value=\"" + currUser.getFullName() + "\">"
content += '''
<input type="hidden" name="reagent_type_hidden" value="Insert">
<table id="vector_insertproperty_table_id" border="1" width="780px" cellpadding="4" frame="box" rules="all">
'''
if errMsg != "":
content += "<th colspan=\"3\" style=\"color:#0000FF; text-align:left; font-weight:normal\">There was a problem:<br><P>" + errMsg + "<BR><BR></th>"
content += '''
<tr>
<td colspan="3" style="text-align:center">
<span style="color:#0000CD; font-size:13pt; font-weight:bold">
Insert Information
</span>
<br>
<span style="font-size:8pt; color:#FF0000">
Fields marked with a red asterisk (*) are mandatory
</span>
</td>
</tr>
<tr>
<td width="180px">
Type of Insert
<span style="font-size:8pt; color:#FF0000; font-weight:bold">*</span>
</td>
<td width="275px">
<SELECT id="itype_list" size="1" NAME="INPUT_INSERT_info_insert_type_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(iType) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for it in iTypeList:
content += "<OPTION VALUE=\"" + it + "\""
if it == iType:
content += " SELECTED>" + it + "</OPTION>"
else:
content += ">" + it + "</OPTION>"
content += '''
</SELECT>
</td>
<td>
Describes the type of insert. Users select from a pre-defined list. Designed to make insert use more apparent and searches easier.
</td>
</tr>
<tr>
<td>
Name
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_name_prop\" value=\"" + iName + "\">"
content += '''
</td>
<td>
Name that describes the reagent - free text field
</td>
</tr>
<tr>
<td>
Status
</td>
<td>
<SELECT id="status_list" name="INPUT_INSERT_info_status_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(iStatus) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for s in statusList:
content += "<OPTION VALUE=\"" + s + "\""
if s == iStatus:
content += " SELECTED>" + s + "</OPTION>"
else:
content += ">" + s + "</OPTION>"
content += '''
</td>
<td>
Indicates the status and availability of the reagent. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Insert Cloning Method
</td>
<td>
<SELECT size="1" id="cm_list" name="INPUT_INSERT_info_cloning_method_prop" onChange="showCMText()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(cloningMethod) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for cm in cloningMethodList:
content += "<OPTION VALUE=\"" + cm + "\""
if cm == cloningMethod:
content += " SELECTED>" + cm + "</OPTION>"
else:
content += ">" + cm + "</OPTION>"
content += '''
</td>
<td>
Describes the method used to create the insert (e.g. PCR or RE (restriction enzyme)) and provides additional information for its cloning into a vector (eg. by RE, In Fusion or BP reaction)
</td>
</tr>
<tr>
<td>
Project ID <span style="font-size:8pt; color:#FF0000; font-weight:bold">*</span>
</td>
<td>
<select id="packetList_insert" size="1" name="INPUT_INSERT_info_packet_id_prop">
'''
# need to sort projects
pNums = []
projects = {} # (pID, Packet)
for p in projectList:
pID = p.getNumber()
pNums.append(pID)
projects[pID] = p
pNums.sort()
for pID in pNums:
p = projects[pID]
content += "<OPTION VALUE=\"" + `p.getNumber()` + "\""
if p.getNumber() == projectID:
content += " SELECTED>" + `p.getNumber()` + ": " + p.getOwner().getLastName() + ": " + p.getName() + "</OPTION>"
else:
content += ">" + `p.getNumber()` + ": " + p.getOwner().getLastName() + ": " + p.getName() + "</OPTION>"
content += '''
</select>
<BR>
<div id="packet_warning_insert" style="display:none; color:#FF0000">Please select a Project ID from the dropdown list</div>
</td>
<td>
Indicates what person and project originally created the reagent.
</td>
</tr>
<tr>
<td>
5' Cloning Site on Insert
</td>
<td>
<SELECT size="1" id="fpcs_list" name="INPUT_INSERT_info_5_prime_cloning_site_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(fpcs) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for fps in fpcsList:
content += "<OPTION VALUE=\"" + fps + "\""
if fps == fpcs:
content += " SELECTED>" + fps + "</OPTION>"
else:
content += ">" + fps + "</OPTION>"
content += '''
</td>
<td>
Indicates what 5' site on the insert was used to clone it into a vector. May not necessarily be the same as for the vector. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
3' Cloning Site on Insert
</td>
<td>
<SELECT size="1" id="tpcs_list" name="INPUT_INSERT_info_3_prime_cloning_site_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tpcs) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tps in tpcsList:
content += "<OPTION VALUE=\"" + tps + "\""
if tps == tpcs:
content += " SELECTED>" + tps + "</OPTION>"
else:
content += ">" + tps + "</OPTION>"
content += '''
</td>
<td>
Indicates what 3' site on the insert was used to clone it into a vector. May not necessarily be the same as for the vector. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Tag
</td>
<td>
<SELECT size="1" id="tag_list" name="INPUT_INSERT_info_tag_prop" onChange="showTagTypeBox()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tagType) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tt in tagTypeList:
content += "<OPTION VALUE=\"" + tt + "\""
if tt == tagType:
content += " SELECTED>" + tt + "</OPTION>"
else:
content += ">" + tt + "</OPTION>"
content += '''
</td>
<td>
Indicates if the insert itself has a tag associated with it (outside of the backbone vector). Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Tag Position
</td>
<td>
<SELECT size="1" name="INPUT_INSERT_info_tag_position_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tagPosition) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tp in tagPositionList:
content += "<OPTION VALUE=\"" + tp + "\""
if tp == tagPosition:
content += " SELECTED>" + tp + "</OPTION>"
else:
content += ">" + tp + "</OPTION>"
content += '''
</td>
<td>
Describes the position of the tag on the insert. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Open/Closed
</td>
<td>
<SELECT id="oc_list" size="1" name="INPUT_INSERT_info_open_closed_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(openClosed) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for oc in openClosedList:
content += "<OPTION VALUE=\"" + oc + "\""
if oc == openClosed:
content += " SELECTED>" + oc + "</OPTION>"
else:
content += ">" + oc + "</OPTION>"
content += '''
</td>
<td>
Indicates for an Open Reading Frame if there is a start codon (ATG) or stop codon (open - no stop codon, closed - stop codon).
</td>
</tr>
<tr>
<td>
Species
</td>
<td>
<SELECT size="1" style="color:000000" id = "species_list" name="INPUT_INSERT_info_species_prop" onChange="showSpeciesBox()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(species) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for sp in speciesList:
content += "<OPTION VALUE=\"" + sp + "\""
if sp == species:
content += " SELECTED>" + sp + "</OPTION>"
else:
content += ">" + sp + "</OPTION>"
content += '''
</td>
<td>
Indicates the species from which the Insert was derived. User selects species from a pre-defined list.
</td>
</tr>
<tr>
<td>
Accession Number
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_accession_number_prop\" value=\"" + accession + "\">"
content += '''
</td>
<td>
The Accession Number from which the insert was cloned or to which the sequence maps.
</td>
</tr>
<tr>
<td>
Alternate ID
</td>
<td>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="IMAGE" id="_alternate_id_IMAGE_checkbox" onClick="showAltIDTextBox('_alternate_id_IMAGE_checkbox', '_alternate_id_IMAGE_textbox')">IMAGE <INPUT style="display:none" id="_alternate_id_IMAGE_textbox" name="alternate_id_IMAGE_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="RIKEN" id="_alternate_id_RIKEN_checkbox" onClick="showAltIDTextBox('_alternate_id_RIKEN_checkbox', '_alternate_id_RIKEN_textbox')">RIKEN <INPUT style="display:none" id="_alternate_id_RIKEN_textbox" name="alternate_id_RIKEN_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="Kazusa" id="_alternate_id_Kazusa_checkbox" onClick="showAltIDTextBox('_alternate_id_Kazusa_checkbox', '_alternate_id_Kazusa_textbox')">Kazusa <INPUT style="display:none" id="_alternate_id_Kazusa_textbox" name="alternate_id_Kazusa_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="LIFESEQ" id="_alternate_id_LIFESEQ_checkbox" onClick="showAltIDTextBox('_alternate_id_LIFESEQ_checkbox', '_alternate_id_LIFESEQ_textbox')">LIFESEQ <INPUT style="display:none" id="_alternate_id_LIFESEQ_textbox" name="alternate_id_LIFESEQ_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="RZPD" id="_alternate_id_RZPD_checkbox" onClick="showAltIDTextBox('_alternate_id_RZPD_checkbox', '_alternate_id_RZPD_textbox')">RZPD <INPUT style="display:none" id="_alternate_id_RZPD_textbox" name="alternate_id_RZPD_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="HIP" id="_alternate_id_HIP_checkbox" onClick="showAltIDTextBox('_alternate_id_HIP_checkbox', '_alternate_id_HIP_textbox')">HIP <INPUT style="display:none" id="_alternate_id_HIP_textbox" name="alternate_id_HIP_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="ADDGENE" id="_alternate_id_ADDGENE_checkbox" onClick="showAltIDTextBox('_alternate_id_ADDGENE_checkbox', '_alternate_id_ADDGENE_textbox')">ADDGENE <INPUT style="display:none" id="_alternate_id_ADDGENE_textbox" name="alternate_id_ADDGENE_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="PMID" id="_alternate_id_PMID_checkbox" onClick="showAltIDTextBox('_alternate_id_PMID_checkbox', '_alternate_id_PMID_textbox')">PMID <INPUT style="display:none" id="_alternate_id_PMID_textbox" name="alternate_id_PMID_textbox_name" size="15"></INPUT><br>
<input type="checkbox" id="_other_Alt_ID_chkbx" name="INPUT_INSERT_info_alternate_id_prop[]" value="Other" onClick="showSpecificOtherCheckbox('_alternate_id_txt')">Other: <INPUT style="display:none" id="_alternate_id_txt" name="alternate_id_name_txt" size="15"></INPUT>
</td>
<td>
Indicates any other ID's that identify the insert, including but not limited to IMAGE, Kazusa, RIKEN, and other. <BR><BR><BR><BR>For 'Other', please enter the source name and ID separated by a semicolon (e.g. IMAGE:123456)
</td>
</tr>
<tr>
<td>
Entrez Gene ID
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_gene_id_prop\" value=\"" + geneID + "\">"
content += '''
</td>
<td>
The NCBI Gene ID to which the sequence maps.
</td>
</tr>
<tr>
<td>
Ensembl Gene ID
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_ensembl_gene_id_prop\" value=\"" + ensemblID + "\">"
content += '''
</td>
<td>
The Ensembl Gene ID to which the sequence maps.
</td>
</tr>
<tr>
<td>
Official Gene Symbol
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_gene_symbol_prop\" value=\"" + geneSymbol + "\">"
content += '''
</td>
<td>
The official gene symbol for this Insert.
</td>
</tr>
<tr>
<td>
5' Start
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_5_prime_start_prop\" value=\"" + fp_start + "\">"
content += '''
</td>
<td>
Users can map the start of the sequence onto its accession number by indicating at what nucleotide position on the accession number that the sequence starts.
</td>
</tr>
<tr>
<td>
3' Stop
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_3_prime_stop_prop\" value=\"" + tp_stop + "\">"
content += '''
</td>
<td>
Users can map the stop of the sequence onto its accession number by indicating at what nucleotide position on the accession number that the sequence stops
</td>
</tr>
<tr>
<td>
5' Linker
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_5_prime_linker_prop\" value=\"" + fwd_linker + "\">"
content += '''
</td>
<td>
Indicates any sequence added to the 5' end of an insert that does not map to a cDNA sequence but should be included as part of the insert - eg kozak sequences, any nucleotides added to maintain frame.
</td>
</tr>
<tr>
<td>
3' Linker
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_3_prime_linker_prop\" value=\"" + rev_linker + "\">"
content += '''
</td>
<td>
Indicates any sequence added to the 3' end of an insert that does not map to a cDNA sequence but should be included as part of the insert - eg any nucleotides added to maintain frame.
</td>
</tr>
<tr>
<td>
Functional Description
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_description_prop\" value=\"" + funcDescr + "\">"
content += '''
</td>
<td>
Describes the purpose of the reagent and any information that may be key to working with the reagent.
</td>
</tr>
<tr>
<td>
Verification
</td>
<td>
<select size="1" name="INPUT_INSERT_info_verification_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(verification) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for v in verificationList:
content += "<OPTION VALUE=\"" + v + "\""
if v == verification:
content += " SELECTED>" + v + "</OPTION>"
else:
content += ">" + v + "</OPTION>"
content += '''
</select>
</td>
<td>
Indicates if the reagent has been verified and how. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Verification comments
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_verification_comments_prop\" value=\"" + verComm + "\">"
content += '''
</td>
<td>
Allows user to provide a description of the verification status - eg comments on sequence changes, expression levels.
</td>
</tr>
<tr>
<td>
Experimental comments
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_comments_prop\" value=\"" + expComm + "\">"
content += '''
</td>
<td>
Used to describe any information that descrbes how the reagent works in the experimental context - eg low expression, difficult to grow, etc.
</td>
</tr>
<tr>
<td>
Sequence
</td>
<td>
</td>
<td>
The sequence of the insert that corresponds to a cDNA or fragment of interest. Does include artificial start and stop codons. Does not include linker sequences as described above.
</td>
</tr>
<tr>
<td colspan="3">
<textarea rows="10" cols="93" id="dna_sequence" name="INPUT_INSERT_info_sequence_prop">
'''
content += sequence
content += '''
</textarea>
</td>
</tr>
'''
content += self.printParents('Insert', allAssoc)
content += '''
<tr>
<td colspan="3">
<hr><br>
<input type="submit" name="create_reagent" value="Create" onclick="document.pressed = this.value">
</td>
</tr>
</table>
</form>
</div>
'''
# Common to all
content += gOut.printFooter()
page_content = content % (hostname + "cgi/create.py")
print "Content-type:text/html" # THIS IS PERMANENT; DO NOT REMOVE
print # DITTO
print page_content
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 printUserInfo(self, cmd, user, errCode=""):
dbConn = DatabaseConn()
hostname = dbConn.getHostname() # to define form action URL
db = dbConn.databaseConnect()
cursor = db.cursor()
uHandler = UserHandler(db, cursor)
lHandler = LabHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
ucMapper = UserCategoryMapper(db, cursor)
category_ID_Name_Map = ucMapper.mapCategoryIDToName()
category_Name_ID_Map = ucMapper.mapCategoryNameToID()
currUser = Session.getUser()
gOut = GeneralOutputClass()
if cmd =='create':
username = user.getUsername()
firstname = user.getFirstName()
lastname = user.getLastName()
email = user.getEmail()
passwd = user.getPassword()
lab = user.getLab()
uLabID = lab.getID()
uLabName = lab.getName()
labs = lHandler.findAllLabs()
# changed Aug. 18/08 - new format
#content = gOut.printHeader() + gOut.printMainMenu()
content = gOut.printHeader()
content += '''
<FORM NAME="create_user_form" METHOD="POST" ACTION="%s" onSubmit="return verifyAddUser();">
<!-- pass current user as hidden form field -->
<INPUT type="hidden" ID="curr_username_hidden" NAME="curr_username"'''
content += "value=\"" + currUser.getFullName() + "\">"
content += '''
<TABLE width="760px" cellpadding="5" cellspacing="5">
<TH colspan="4" style="color:#0000FF; border-top:1px groove black; border-bottom: 1px groove black; padding-top: 10px; padding-top:5px;">
ADD NEW USER
<P style="color:#FF0000; font-weight:normal; font-size:8pt; margin-top:5px;">Fields in red marked with an asterisk (<span style="font-size:9pt; color:#FF0000;">*</span>) are mandatory</P>
</TH>
<TR>
<TD style="width:150px; vertical-align:top; padding-top:10px; color:#FF0000;">
Laboratory: <sup style="font-size:10pt; color:#FF0000;">*</sup>
</TD>
<TD style="vertical-align:top; padding-top:10px">
<SELECT id="labList" name="labs">
<OPTION>Select Lab</OPTION>
'''
# sort labs by name
labSortedDict = {} # will store (labName, labID) tuples
labNames = [] # just hold lab names
for labID in labs.keys():
labName = labs[labID]
labNames.append(labName)
labSortedDict[labName] = labID
labNames.sort()
#for labID in labs.keys():
for labName in labNames:
labID = labSortedDict[labName]
labName = labs[labID]
content += "<OPTION ID=\"" + `labID` + "\" NAME=\"lab_optn\" VALUE=\"" + `labID` + "\""
if labID == uLabID:
content += " SELECTED>" + labName
else:
content += ">" + labName
content += "</OPTION>"
content += '''
</SELECT>
<BR/>
<P id="lab_warning" style="color:#FF0000; display:none">Please select a laboratory name from the dropdown list above.</P>
</TD>
</TR>
<TR>
<TD class="createViewColName" style="color:#FF0000;">
Username: <sup style="font-size:10pt; color:#FF0000;">*</sup>
</TD>
<TD class="createViewColValue">
<INPUT TYPE="TEXT" SIZE="35px" id="user_name" NAME="username" VALUE="%s"/>
<BR/>
<!-- Warning anchor -->
<a name="w1" style="text-decoration:none; font-weight:normal; font-size:8pt">
<P id="dup_uname_warning" style="color:#FF0000; display:inline">This username already exists. Please specify a different username.</P>
</a>
</TD>
<TD style="font-size:8pt">
Alphanumeric string up to 10 characters used to log into the system.
</TD>
</TR>
<TR>
<TD class="createViewColName" style="color:#FF0000;">
Password: <sup style="font-size:10pt; color:#FF0000;">*</sup>
</TD>
<TD class="createViewColValue">
<INPUT TYPE="PASSWORD" SIZE="35px" id="passwd" NAME="password" VALUE="%s"/>
</TD>
</TR>
<TR>
<TD class="createViewColName" style="color:#FF0000;">
First name: <sup style="font-size:10pt; color:#FF0000;">*</sup>
</TD>
<TD class="createViewColValue">
<INPUT TYPE="TEXT" SIZE="35px" id="first_name" NAME="firstName" VALUE="%s"/>
</TD>
</TR>
<TR>
<TD class="createViewColName" style="color:#FF0000;">
Last name: <sup style="font-size:10pt; color:#FF0000;">*</sup>
</TD>
<TD class="createViewColName">
<INPUT TYPE="TEXT" SIZE="35px" id="last_name" NAME="lastName" VALUE="%s"/>
</TD>
</TR>
<TR>
<TD class="createViewColName">
Email:
</TD>
<TD class="createViewColValue">
<INPUT TYPE="TEXT" SIZE="35px" id="e_mail" NAME="email" VALUE="%s"/>
</TD>
</TR>
<TR>
<TD>
Access Level:
</TD>
<TD class="createViewColName" colspan="3">
<INPUT TYPE="RADIO" name="system_access_level" value="Reader" style="margin-top:8px; font-size:9pt" checked>Reader<BR/>
<INPUT TYPE="RADIO" name="system_access_level" value="Writer" style="margin-top:8px; font-size:9pt">Writer<BR/>
<INPUT TYPE="RADIO" name="system_access_level" value="Creator" style="margin-top:8px; font-size:9pt">Creator<BR/>
<INPUT TYPE="RADIO" name="system_access_level" value="Admin" style="margin-top:8px; font-size:9pt">Admin<BR/>
</TD>
</TR>
<TR id="project_access">
<TD colspan="4">
<TABLE width="100%%">
<TR>
<TD colspan="4" style="border-top:1px groove black; border-bottom:1px groove black; padding-top:8px; font-size:8pt; font-weight:bold">
Grant project access permissions to this user:
</TD>
</TR>
<TR>
<TD style="width:210px">
<SELECT id="packetList" name="packets" multiple size="15">
'''
# PRINT PROJECT LIST
projects = pHandler.findAllProjects()
for project in projects:
projectNumber = project.getNumber()
projectName = project.getName()
tmpProject = `projectNumber` + ": " + projectName
content += "<OPTION value=\"" + `projectNumber` + "\">" + tmpProject + "</OPTION>"
content += '''
</SELECT>
<BR/>
<INPUT TYPE="checkbox" style="margin-top:10px; font-size:8pt;" onClick="selectAll(this.id, 'packetList')" id="add_all_chkbx"> Select All</INPUT>
</TD>
<TD style="vertical-align:top" colspan="3">
<span style="font-size:8pt; font-weight:bold">User's access level to selected projects:<BR/></span>
<input type="radio" id="access_level_radio_read" name="access_levels" value="read" style="margin-top:8px; font-size:9pt" checked>Read-Only <BR/>
<input type="radio" id="access_level_radio_write" name="access_levels" value="write" style="margin-top:5px; font-size:9pt">Write <BR/>
<input style="margin-top:8px" onclick="addProjects('packetList', getSelectedRole('1'))" value="Go" type="button"></INPUT>
<P style="font-size:8pt; border-top:1px groove black; padding-top:10px; padding-bottom:5px; margin-top:10px">
Access levels: <BR/>
<span style="font-size: 8pt; margin-left: 9px; font-weight:bold; ">- Read-Only:</span> May view reagents in a project but may NOT modify them or add new reagents<BR/>
<span style="font-size: 8pt; margin-left: 9px; font-weight:bold;">- Write:</span> May create and modify reagents in a project but may NOT change project details or add/remove members to/from the project<BR/>
</P>
</TD>
</TR>
<TR>
<TD colspan="4" style="border-top:1px groove black; border-bottom:1px groove black; font-size:8pt; font-weight:bold">
User's current project access privileges:
</TD>
</TR>
<TR>
<TD style="border-right:1px solid black; font-size:8pt">
<B>Read-Only</B><BR/>
<SELECT id="user_projects_readonly" name="userProjectsReadonly" style="margin-top:5px" multiple size="12">
'''
# August 10/07: Default reader access to all on public projects
publicProjects = pHandler.findAllProjects('FALSE')
for proj in publicProjects:
pID = proj.getNumber()
pName = proj.getName();
# concatenate project ID and name in the form '1:parent'
tmpDescr = `pID` + ": " + pName
content += "<OPTION VALUE=\"" + `pID` + "\">" + tmpDescr + "</OPTION>"
content += '''
</SELECT><BR/>
<INPUT style="margin-top:10px;" TYPE="checkbox" onClick="selectAll(this.id, 'user_projects_readonly')" id="select_all_reader_chkbx"> Select All</INPUT>
</TD>
<TD style="text-align:center; width:100px; border-right: 1px solid black; padding-left:20px; padding-right:20px;">
<input onclick="addProjects('user_projects_readonly', 'write')" value=" Make Writeable >>" type="button"></INPUT><BR/>
<input style="margin-top:30px;" onclick="addProjects('user_projects_write', 'read')" value="<< Make Read-Only" type="button"></INPUT><BR/>
<input style="margin-top:30px;" onclick="addProjects('user_projects_write'); addProjects('user_projects_readonly')" value="Remove Selected" type="button"></INPUT>
</TD>
<TD style="padding-left:50px; font-size:8pt">
<B>Write</B><BR/>
<SELECT id="user_projects_write" name="userProjectsWrite" style="margin-top:5px" multiple size="12"></SELECT><BR/>
<INPUT style="margin-top:10px;" TYPE="checkbox" onClick="selectAll(this.id, 'user_projects_write')" id="select_all_writer_chkbx"> Select All</INPUT>
</TD>
</TR>
</TABLE>
</TD>
</TR>
<TR>
<TD colspan="4" style="border-top:1px groove black; border-bottom:1px groove black">
<INPUT TYPE="SUBMIT" id="addUser" NAME="add_user" VALUE="Add User" onClick="selectAllElements('user_projects_readonly'); selectAllElements('user_projects_write');">
</TD>
</TR>
</TABLE>
</FORM>
<blockquote> </blockquote>
<blockquote> </blockquote>
</div>
'''
content += gOut.printFooter()
page_content = content % (hostname + "cgi/user_request_handler.py", username, passwd, firstname, lastname, email)
print "Content-type:text/html" # THIS IS PERMANENT; DO NOT REMOVE
print # DITTO
print page_content
elif cmd == 'view':
userID = user.getUserID()
username = user.getUsername()
firstname = user.getFirstName()
lastname = user.getLastName()
email = user.getEmail()
userCat = user.getCategory()
lab = user.getLab()
labID = lab.getID()
labName = lab.getName()
# Only allow modification by admin
modify_disabled = True
if (currUser.getCategory() == 'Admin'):
modify_disabled = False
content = gOut.printHeader()
#content += gOut.printMainMenu()
content += '''
<FORM name="user_form" method="POST" action="%s">
<!-- pass current user as hidden form field -->
<INPUT type="hidden" ID="curr_username_hidden" NAME="curr_username"'''
content += "value=\"" + currUser.getFullName() + "\">"
content += '''
<TABLE width="767px" style="margin-left:2px" cellpadding="5px" cellspacing="5px" class="detailedView_tbl" border="1" frame="box" rules="none">
<TR>
<TD colspan="6" class="detailedView_heading" style="padding-left:265px">
USER DETAILS PAGE
'''
content += "<INPUT TYPE=\"submit\" style=\"margin-left:50px;\" name=\"modify_user\" value=\"Change User Details\""
if modify_disabled:
content += " disabled>"
else:
content += ">"
content += "<INPUT TYPE=\"submit\" style=\"margin-left:2px;\" name=\"delete_user\" value=\"Delete User\" onClick=\"return verifyDeleteUser();\""
if modify_disabled:
content += " disabled>"
else:
content += ">"
content += '''
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName" width="50px">
Username:
</TD>
<TD class="detailedView_value" colspan="2" style="width:400px">
%s
<INPUT TYPE="hidden" name="username" value="%s">
<!-- user ID a hidden value -->
<INPUT TYPE="hidden" name="userID" value="%d">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName" width="50px">
First Name:
</TD>
<TD class="detailedView_value" colspan="2" style="width:400px">
%s
<INPUT TYPE="hidden" name="firstName" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName" width="50px">
Last Name:
</TD>
<TD class="detailedView_value" colspan="2" style="width:400px">
%s
<INPUT TYPE="hidden" name="lastName" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName" width="50px">
Laboratory:
</TD>
<TD class="detailedView_value" colspan="2" style="width:400px">
'''
if modify_disabled:
content += labName
else:
content += "<span class=\"linkShow\" onClick=\"redirectToLabView(" + `labID` + ");\">" + labName + "</span>"
content += '''
<INPUT TYPE="hidden" name="labID" value="%d">
<INPUT type="hidden" id="view_lab_hidden" name="view_lab">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName" width="50px">
Email:
</TD>
<TD class="detailedView_value" colspan="2" style="width:400px">
%s
<INPUT TYPE="hidden" name="email" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName" width="50px">
Access Level:
</TD>
<TD class="detailedView_value" colspan="2" style="width:400px">
%s
<INPUT TYPE="hidden" name="system_access_level" value="%d">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName" width="50px">
Projects:
</TD>
</TR>
<TR>
<TD style="font-weight:bold; font-size:8pt; width:250px" colspan="2">
Read-Only:
</TD>
<TD style="font-weight:bold; font-size:8pt">
Write:
</TD>
</TR>
<TR>
<TD style="vertical-align:top;" colspan="2">
<UL>
'''
# show projects for the user
publicProj = pHandler.findAllProjects("FALSE")
readOnlyProj = pHandler.findMemberProjects(userID, 'Reader')
readProj = utils.merge(publicProj, readOnlyProj)
writeProj = pHandler.findMemberProjects(userID, 'Writer')
# sort read projects
readKeys = []
readSorted = {}
for r in readProj:
rProjectID = r.getNumber()
readKeys.append(rProjectID)
readSorted[rProjectID] = r
readKeys = utils.unique(readKeys)
readKeys.sort()
#for r in readProj:
for rProjectID in readKeys:
#rProjectID = r.getNumber()
r = readSorted[rProjectID]
rProjectName = r.getName()
rProjectOwner = r.getOwner()
try:
rOwnerName = rProjectOwner.getLastName()
except AttributeError:
rOwnerName = ""
#content += "<LI>" + `rProjectID` + ": " + rOwnerName + ": " + rProjectName
content += "<LI>"
content += "<span class=\"linkShow\" onClick=\"redirectToProjectDetailedView(" + `rProjectID` + ");\">" + `rProjectID` + ": " + rOwnerName + ": " + rProjectName + "</span>"
content += "</LI>"
content += '''
</UL>
</TD>
<TD style="vertical-align:top;">
<UL>
'''
# sort write projects
writeKeys = []
writeSorted = {}
for w in writeProj:
wProjectID = w.getNumber()
writeKeys.append(wProjectID)
writeSorted[wProjectID] = w
writeKeys = utils.unique(writeKeys)
writeKeys.sort()
#for w in writeProj:
for wProjectID in writeKeys:
#wProjectID = w.getNumber()
w = writeSorted[wProjectID]
wProjectName = w.getName()
wProjectOwner = w.getOwner()
wOwnerName = wProjectOwner.getLastName()
#content += "<LI>" + `wProjectID` + ": " + wProjectName
content += "<LI>"
content += "<span class=\"linkShow\" onClick=\"redirectToProjectDetailedView(" + `wProjectID` + ");\">" + `wProjectID` + ": " + wOwnerName + ": " + wProjectName + "</span>"
content += "</LI>"
content += '''
</UL>
</TD>
</TR>
</TABLE>
</FORM>
<FORM id="viewProjectForm" method="POST" action="%s">
<INPUT type="hidden" id="view_packet_hidden" name="view_packet">
<INPUT type="hidden" ID="curr_userid_hidden" NAME="curr_user_id" value="%d">
</FORM>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
</div>
'''
content += gOut.printFooter()
page_content = content % (hostname + "cgi/user_request_handler.py", username, username, userID, firstname, firstname, lastname, lastname, labID, email, email, userCat, category_Name_ID_Map[userCat], hostname + "cgi/project_request_handler.py", currUser.getUserID())
print "Content-type:text/html" #
print # DITTO
print page_content
elif cmd == 'edit':
userID = user.getUserID()
username = user.getUsername()
firstname = user.getFirstName()
lastname = user.getLastName()
email = user.getEmail()
passwd = user.getPassword()
userCat = user.getCategory()
lab = user.getLab()
uLabID = lab.getID()
labName = lab.getName()
labs = lHandler.findAllLabs()
if errCode == "Dup_un":
un_warn_display = "inline"
else:
un_warn_display = "none"
content = gOut.printHeader()
#content += gOut.printMainMenu()
content += '''
<FORM name="user_form" method="POST" action="%s" onSubmit="return verifyWriteProjects();">
<!-- pass current user as hidden form field -->
<INPUT type="hidden" ID="curr_username_hidden" NAME="curr_username"'''
content += "value=\"" + currUser.getFullName() + "\">"
content += '''
<TABLE width="760px" cellpadding="5px" cellspacing="5px" style="border:1px solid black" frame="box" rules="rows">
<TR>
<TD colspan="3" style="padding-left:200px; text-align:center">
<span style="color:#0000FF; font-weight:bold">CHANGE USER INFORMATION</span>
<INPUT TYPE="submit" style="margin-left:50px;" name="save_user" value="Save" onClick="selectAllElements('user_projects_readonly'); selectAllElements('user_projects_write');">
<INPUT TYPE="submit" style="margin-left:20px;" name="cancel_user" value="Cancel">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Username:
</TD>
<TD class="detailedView_value" style="width:400px">
<INPUT TYPE="text" size="50px" name="username" value="%s">
<BR/>
<!-- Warning anchor -->
<a name="w1" style="text-decoration:none; font-weight:normal; font-size:8pt">
<P id="dup_uname_warning" style="color:#FF0000; display:%s">This username already exists. Please specify a different username.</P>
</a>
<!-- user ID hidden value -->
<INPUT TYPE="hidden" name="userID" value="%d">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Laboratory:
</TD>
<TD style="vertical-align:top; padding-top:10px">
<SELECT id="labList" name="labs">
'''
# sort labs by name
labSortedDict = {} # will store (labName, labID) tuples
labNames = [] # just hold lab names
for labID in labs.keys():
labName = labs[labID]
labNames.append(labName)
labSortedDict[labName] = labID
labNames.sort()
#for labID in labs.keys():
for labName in labNames:
labID = labSortedDict[labName]
labName = labs[labID]
content += "<OPTION ID=\"" + `labID` + "\" NAME=\"lab_optn\" VALUE=\"" + `labID` + "\""
if labID == uLabID:
content += " SELECTED>" + labName
else:
content += ">" + labName
content += "</OPTION>"
content += '''
</SELECT>
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
First Name:
</TD>
<TD class="detailedView_value" colspan="2">
<INPUT TYPE="text" size="50px" name="firstName" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Last Name:
</TD>
<TD class="detailedView_value" colspan="2">
<INPUT TYPE="text" size="50px" name="lastName" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Email:
</TD>
<TD class="detailedView_value" colspan="2">
<INPUT TYPE="text" size="50px" name="email" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Access Level:
</TD>
<TD class="detailedView_value" colspan="2">
<SELECT ID="user_category" NAME="system_access_level">
'''
ucHandler = UserCategoryHandler(db, cursor)
categories = ucHandler.findAllCategories()
for cID in categories.keys():
if categories[cID] == userCat:
content += "<OPTION VALUE=\"" + `cID` + "\" SELECTED>" + categories[cID] + "</OPTION>"
else:
content += "<OPTION VALUE=\"" + `cID` + "\">" + categories[cID] + "</OPTION>"
# Don't allow addition of Writeable projects to Readers thru Modify view
if userCat == 'Reader':
write_disabled = True
else:
write_disabled = False
content += '''
</SELECT>
</TD>
</TR>
<TR>
<TD class="detailedView_value" colspan="3">
Projects user has access to:
</TD>
</TR>
<TR>
<td colspan="3">
<table width="700px">
<tr>
<TD colspan="2" style="font-size:8pt; vertical-align:top"">
Read-Only
</TD>
<TD style="font-size:8pt; vertical-align:top">
'''
if not write_disabled:
content += "Write"
else:
content += " "
content += '''
</TD>
</TR>
<TR>
<TD style="">
<SELECT id="user_projects_readonly" name="userProjectsReadonly" style="margin-top:5px" multiple size="12">
'''
# show projects for the user
readProj = pHandler.findMemberProjects(userID, 'Reader')
writeProj = pHandler.findMemberProjects(userID, 'Writer')
for r in readProj:
rProjectID = r.getNumber()
rProjectName = r.getName()
content += "<OPTION name=\"project_read\" value=\"" + `rProjectID` + "\">" + `rProjectID` + ": " + rProjectName + "</OPTION>"
content += '''
</SELECT>
<BR/>
<INPUT TYPE="checkbox" style="margin-top:10px;" onClick="selectAll(this.id, 'user_projects_readonly')" id="select_all_reader_chkbx"> Select All</INPUT>
'''
if not write_disabled:
content += '''
</TD>
<TD style="text-align:center; padding-right:15px;">
<input onclick="addProjects('user_projects_readonly', 'write')" value=" Make Writeable >>" type="button"></INPUT><BR/>
<input style="margin-top:30px;" onclick="addProjects('user_projects_write', 'read')" value="<< Make Read-Only" type="button"></INPUT><BR/>
<input type="button" style="margin-top:30px;" value="Remove" onclick="removeUserProjects();"></INPUT>
</TD>
'''
else:
content += '''
<input type="button" value="Remove Selected" onclick="removeUserProjects();"></INPUT>
'''
if not write_disabled:
content += '''
<TD style="font-size:8pt">
<SELECT id="user_projects_write" name="userProjectsWrite" style="margin-top:5px" multiple size="12">
'''
for w in writeProj:
wProjectID = w.getNumber()
wProjectName = w.getName()
content += "<OPTION name=\"project_write\" value=\"" + `wProjectID` + "\">" + `wProjectID` + ": " + wProjectName + "</OPTION>"
content += '''
</SELECT><BR/>
<INPUT style="margin-top:10px;" TYPE="checkbox" onClick="selectAll(this.id, 'user_projects_write')" id="select_all_writer_chkbx"> Select All</INPUT>
</TD>
'''
content += '''
</TR>
</table>
</td>
</tr>
<TR>
<TD class="detailedView_value" colspan="3">
Add new projects:
</TD>
</TR>
<TR>
<TD colspan="3">
<TABLE>
<TR>
<TD>
<SELECT multiple ID="packetList">
'''
# Fetch the list of read and write projects for this user and extract their IDs
readProjID = [] # list of numerical IDs of read projects
for r in readProj:
rNum = r.getNumber()
readProjID.append(rNum)
writeProjID = []
for w in writeProjID:
wNum = w.getNumber()
writeProjID.append(wNum)
allPackets = pHandler.findAllProjects()
for p in allPackets:
pID = p.getNumber()
pName = p.getName()
pOwner = p.getOwner()
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `pOwner`
# update March 11, 2011
try:
lastName = pOwner.getLastName()
except AttributeError:
lastName = ""
#pDesc = `pID` + " : " + pOwner + " : " + pName
pDesc = `pID` + " : " + lastName + " : " + pName
if not pID in readProjID and not pID in writeProjID:
content += "<OPTION VALUE=\"" + `pID` + "\">" + pDesc
content += '''
</SELECT>
<BR>
<INPUT TYPE="checkbox" style="margin-top:10px; font-size:8pt;" onClick="selectAll(this.id, 'packetList')" id="add_all_chkbx"> Select All</INPUT>
'''
if not write_disabled:
content += '''
</TD>
<TD style="vertical-align:top">
<span style="font-size:8pt; font-weight:bold">User's access level to selected projects:<BR/></span>
<input type="radio" id="access_level_radio_read" name="access_levels" value="read" style="margin-top:8px; font-size:9pt" checked>Read-Only <BR/>
<input type="radio" id="access_level_radio_write" name="access_levels" value="write" style="margin-top:5px; font-size:9pt">Write <BR/>
<input style="margin-top:8px" onclick="addProjects('packetList', getSelectedRole('1'))" value="Add project" type="button"></INPUT>
</TD>
</TABLE>
</TD>
</TR>
'''
else:
content += '''
<input style="margin-left:5px; margin-top:8px" onclick="addProjects('packetList', 'read')" value="Add project" type="button"></INPUT>
'''
content += '''
</TR>
</TABLE>
</FORM>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
</div>
'''
content += gOut.printFooter()
page_content = content % (hostname + "cgi/user_request_handler.py", username, un_warn_display, userID, firstname, lastname, email)
print "Content-type:text/html" # THIS IS PERMANENT; DO NOT REMOVE
print # DITTO
print page_content
def addUser(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
mail_server = self.__mail_server # August 19, 2011
mail_programmer = self.__mail_programmer # July 30, 2010
mail_biologist = self.__mail_biologist
mail_admin = self.__mail_admin
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
uHandler = UserHandler(db, cursor)
lHandler = LabHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
ucMapper = UserCategoryMapper(db, cursor)
category_Name_ID_Map = ucMapper.mapCategoryNameToID()
# Get form values
labID = int(form.getvalue("labs"))
username = form.getvalue("username")
firstName = form.getvalue("firstName")
lastName = form.getvalue("lastName")
description = firstName + " " + lastName
to_email = form.getvalue("email")
from_email = mail_admin
# Change July 30, 2010 - random password generator
#passwd = form.getvalue("password")
chars = string.letters + string.digits
passwd = ""
for i in range(10):
passwd += choice(chars)
# System access level: Lab default or override?
#if form.getvalue("privChoiceRadio") == 'override':
accessLevel = category_Name_ID_Map[form.getvalue(
"system_access_level")]
#else:
#accessLevel = lHandler.findDefaultAccessLevel(labID)
newProps = {}
try:
# Insert User information
userID = uHandler.insertUser(username, firstName, lastName,
description, accessLevel, to_email,
passwd, labID)
#newUser = uHandler.getUserByID(userID)
tmpLab = lHandler.findLabByID(labID)
#print tmpLab.getName()
# Insert Project info
# Sept. 11/07: Differentiate between user categories Reader and Writer - different field names
if form.has_key("userProjectsReadonly"):
# list of IDs
readonlyProjects = utils.unique(
form.getlist("userProjectsReadonly"))
#print `readonlyProjects`
pHandler.insertMemberProjects(userID, readonlyProjects,
'Reader')
elif form.has_key("userProjectsReadonlyWrite"):
# list of IDs
readonlyProjects = utils.unique(
form.getlist("userProjectsReadonlyWrite"))
#print `readonlyProjects`
pHandler.insertMemberProjects(userID, readonlyProjects,
'Reader')
# Write projects exist only for Writers
if form.has_key("userProjectsWrite"):
writeProjects = utils.unique(form.getlist("userProjectsWrite"))
pHandler.insertMemberProjects(userID, writeProjects, 'Writer')
# don't assign projects to a User instance - will retrieve them from db in output function
newUser = User(userID, username, firstName, lastName,
description, tmpLab,
form.getvalue("system_access_level"), to_email,
passwd, [], [])
email_subject = "OpenFreezer User Account"
msg = email.MIMEMultipart.MIMEMultipart('alternative')
msg['Subject'] = email_subject
msg['To'] = to_email
msgText = "Hi " + firstName + ",<BR><BR>An OpenFreezer account has been created for you. Your access level is " + form.getvalue(
"system_access_level") + ", so you can "
if form.getvalue("system_access_level") == 'Reader':
msgText += "search for clones. If you wish to add/modify reagents or create projects, please contact the administrator to upgrade your access level.<BR>"
elif form.getvalue("system_access_level") == 'Writer':
msgText += "search, add, and modify reagents. If you wish to create projects, please contact the administrator to upgrade your access level.<BR>"
elif form.getvalue("system_access_level") == 'Creator':
msgText += "search for clones, add and modify reagents, as well as create your own projects.<BR>"
#####################################################
# CHANGE TEXT AS NEEDED
#####################################################
msgText += "<BR>The URL to access the system is <a href='" + hostname + "'>" + hostname + "</a>. Your username is <b>" + username + "</b>, and your temporary password is <b>" + passwd + "</b>. Please <u>change the temporary password as soon as you log into the website</u> - you can do it through the 'Change your password' link under the 'User Management' menu section.<BR><BR>Please refer to http://openfreezer.org for additional support.<BR><BR>Sincerely,<BR>OpenFreezer support team.<BR><BR><span style='font-family:Courier; font-size:10pt;'><HR>This is an automatically generated e-mail message. Please do not reply to this e-mail. All questions should be directed to your local administrator.</span>"
msgText = email.MIMEText.MIMEText(msgText, 'html')
msg.attach(msgText)
server = smtplib.SMTP(mail_server)
server.set_debuglevel(1)
server.sendmail(from_email, [to_email], msg.as_string())
server.quit()
self.printUserInfo('view', newUser)
except DeletedUserException:
# Without asking too many questions, reactivate the deleted user and overwrite his/her attributes with the form input values
userID = uHandler.findUserIDByUsername(username)
newProps["firstname"] = firstName
newProps["lastname"] = lastName
newProps["description"] = description
newProps["email"] = email
newProps["status"] = "ACTIVE"
newProps["password"] = passwd
# Insert new database values and create new object
uHandler.updateUserProperties(userID, newProps) # database update
newUser = uHandler.getUserByID(userID)
# Insert Project info
readProjects = []
writeProjects = []
if form.has_key("userProjectsReadonly"):
# list of IDs
readonlyProjects = form.getlist("userProjectsReadonly")
for r in readonlyProjects:
pHandler.addProjectMember(r, userID, 'Reader')
#tmpReadProject = pHandler.findPacket(r)
#readProjects.append(tmpReadProject)
#newUser.addProject(tmpReadProject, 'read')
if form.has_key("userProjectsWrite"):
writeProjects = form.getlist("userProjectsWrite")
for w in writeProjects:
pHandler.addProjectMember(w, userID, 'Writer')
#tmpWriteProject = pHandler.findPacket(w)
#writeProjects.append(tmpWriteProject)
#newUser.addProject(tmpWriteProject, 'write')
#newUser.setReadProjects(readProjects)
#newUser.setWriteProjects(writeProjects)
self.printUserInfo('view', newUser)
#utils.redirect(hostname + "User.php?View=3&fd=" + filename)
except DuplicateUsernameException:
# return to the view with input values and error message
# Need to construct a dummy User instance to save form values for error output on the next page (otherwise they're lost as soon as Submit is pressed and creation view is exited)
newLab = lHandler.findLabByID(labID)
newUser = User(0, username, firstName, lastName, description,
newLab, "", email, passwd)
self.printUserInfo('create', newUser)
def saveProject(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
# Handlers
pHandler = ProjectDatabaseHandler(db, cursor)
uHandler = UserHandler(db, cursor)
# Get project ID from form
projectID = form.getvalue("packetID")
ownerID = form.getvalue("packetOwner")
# get owner's name
packetOwner = uHandler.getUserByID(ownerID)
packetName = form.getvalue("packetName")
packetDescription = form.getvalue("packetDescription")
# private or public
if form.getvalue("private_or_public") == "public":
isPrivate = False
else:
isPrivate = True
# Lists of project readers & editors
# Updated Sept. 3/08: Do NOT save readers for a public project
if isPrivate:
projectReaderIDs = form.getlist("readersList")
else:
projectReaderIDs = []
# writers are always needed
projectWriterIDs = form.getlist("writersList")
projectReaders = []
projectWriters = []
for rID in projectReaderIDs:
tmpReader = uHandler.getUserByID(rID)
projectReaders.append(tmpReader)
for wID in projectWriterIDs:
tmpWriter = uHandler.getUserByID(wID)
# check categories - a Reader cannot be given Write access to a project
if tmpWriter.getCategory() != 'Reader':
projectWriters.append(tmpWriter)
#projectWriters.append(tmpWriter)
# Update database values
pHandler.updatePacket(projectID, ownerID, packetName, packetDescription, isPrivate, projectReaderIDs, projectWriterIDs)
# Output new values
newProject = Packet(projectID, packetName, packetDescription, packetOwner, isPrivate, projectReaders, projectWriters)
self.showProjectDetails('view', newProject)
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 saveUser(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
uHandler = UserHandler(db, cursor)
lHandler = LabHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
ucMapper = UserCategoryMapper(db, cursor)
category_ID_Name_Map = ucMapper.mapCategoryIDToName()
newProps = {}
# Get form values
userID = int(form.getvalue("userID"))
newUser = uHandler.getUserByID(userID)
labID = int(form.getvalue("labs"))
tmpLab = lHandler.findLabByID(labID)
# rest of user properties
username = form.getvalue("username")
firstName = form.getvalue("firstName")
lastName = form.getvalue("lastName")
description = firstName + " " + lastName
email = form.getvalue("email")
category = category_ID_Name_Map[int(
form.getvalue("system_access_level"))]
newProps["labID"] = labID
newProps["username"] = username
newProps["firstname"] = firstName
newProps["lastname"] = lastName
newProps["description"] = description
newProps["email"] = email
newProps["category"] = category
try:
# Now do an update on database level AND on class level:
uHandler.updateUserProperties(userID, newProps) # database update
# Interface level
newUser.setUsername(username)
newUser.setFirstName(firstName)
newUser.setLastName(lastName)
newUser.setDescription(description)
newUser.setEmail(email)
newUser.setLab(tmpLab)
newUser.setCategory(category)
# update list of user's projects
if form.has_key("userProjectsReadonly"):
# list of IDs
readonlyProjects = utils.unique(
form.getlist("userProjectsReadonly"))
pHandler.updateUserProjects(userID, readonlyProjects, 'Reader')
else:
# safe to assume should delete projects?
pHandler.deleteMemberProjects(userID, 'Reader')
if form.has_key("userProjectsWrite"):
writeProjects = utils.unique(form.getlist("userProjectsWrite"))
pHandler.updateUserProjects(userID, writeProjects, 'Writer')
else:
# safe to assume should delete projects?
pHandler.deleteMemberProjects(userID, 'Writer')
# think about this
#newUser.setReadProjects(readProjects)
#newUser.setWriteProjects(writeProjects)
# return to detailed view
self.printUserInfo('view', newUser)
#utils.redirect(hostname + "User.php?View=3&fd=" + filename)
except DuplicateUsernameException:
# return to the view with input values and error message
# Need to construct a dummy User instance to save form values for error output on the next page (otherwise they're lost as soon as Submit is pressed and creation view is exited)
newLab = lHandler.findLabByID(labID)
newUser = User(userID, username, firstName, lastName, description,
newLab, category, email, "")
self.printUserInfo('edit', newUser, "Dup_un")
from session import Session # make global?? dbConn = DatabaseConn() db = dbConn.databaseConnect() hostname = dbConn.getHostname() cursor = db.cursor() # Handlers and Mappers aHandler = AssociationHandler(db, cursor) rHandler = ReagentHandler(db, cursor) iHandler = InsertHandler(db, cursor) raHandler = ReagentAssociationHandler(db, cursor) sHandler = DNAHandler(db, cursor) pHandler = ReagentPropertyHandler(db, cursor) packetHandler = ProjectDatabaseHandler(db, cursor) uHandler = UserHandler(db, cursor) rtPropHandler = ReagentTypePropertyHandler(db, cursor) oHandler = OligoHandler(db, cursor) propMapper = ReagentPropertyMapper(db, cursor) aMapper = ReagentAssociationMapper(db, cursor) rMapper = ReagentTypeMapper(db, cursor) # Various maps reagentType_Name_ID_Map = rMapper.mapTypeNameID() reagentType_ID_Name_Map = rMapper.mapTypeIDName() assoc_Type_Name_Map = aMapper.mapAssocTypeNameID() assoc_Name_Alias_Map = aMapper.mapAssocNameAlias()
def printReagentInfo(self, cmd, reagent, errMsg=""):
dbConn = DatabaseConn()
hostname = dbConn.getHostname() # to define form action URL
db = dbConn.databaseConnect()
cursor = db.cursor()
gOut = GeneralOutputClass()
currUser = Session.getUser()
currUserID = currUser.getUserID()
sHandler = SystemSetHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
# print menu
content = gOut.printHeader() + gOut.printMainMenu()
# common to all reagent types
projectList = utils.unique(
pHandler.findMemberProjects(currUserID, 'Writer') +
pHandler.findMemberProjects(currUserID, 'Owner'))
# Differentiate other properties by reagent type
if reagent.getType() == 'Insert':
# Fetch dropdown list values to output on the form
iTypeList = sHandler.findAllSetValues("type of insert")
statusList = sHandler.findAllSetValues("status")
cloningMethodList = sHandler.findAllSetValues(
"insert cloning method")
fpcsList = sHandler.findAllSetValues("5' cloning site")
tpcsList = sHandler.findAllSetValues("3' cloning site")
tagTypeList = sHandler.findAllSetValues("tag")
tagPositionList = sHandler.findAllSetValues("tag position")
openClosedList = sHandler.findAllSetValues("open/closed")
speciesList = sHandler.findAllSetValues("species")
verificationList = sHandler.findAllSetValues("verification")
# Initialize property values
iType = ""
iName = ""
iStatus = ""
cloningMethod = ""
projectID = ""
fpcs = ""
tpcs = ""
tagType = ""
tagPosition = ""
openClosed = ""
species = ""
accession = ""
altID = ""
geneID = ""
ensemblID = ""
geneSymbol = ""
fp_start = ""
tp_stop = ""
fwd_linker = ""
rev_linker = ""
funcDescr = ""
verification = ""
expComm = ""
verComm = ""
sequence = ""
# Fetch POST values if available:
allProps = reagent.getProperties()
if allProps.has_key("type of insert"):
iType = allProps["type of insert"]
if allProps.has_key("name"):
iName = allProps["name"]
if allProps.has_key("status"):
iStatus = allProps["status"]
if allProps.has_key("insert cloning method"):
cloningMethod = allProps["insert cloning method"]
if allProps.has_key("packet id"):
projectID = int(allProps["packet id"])
if allProps.has_key("5' cloning site"):
fpcs = allProps["5' cloning site"]
if allProps.has_key("3' cloning site"):
tpcs = allProps["3' cloning site"]
if allProps.has_key("tag"):
tagType = allProps["tag"]
if allProps.has_key("tag position"):
tagPosition = allProps["tag position"]
if allProps.has_key("open/closed"):
openClosed = allProps["open/closed"]
if allProps.has_key("species"):
species = allProps["species"]
if allProps.has_key("accession number"):
accession = allProps["accession number"]
if allProps.has_key("alternate id"):
altID = allProps["alternate id"]
if allProps.has_key("entrez gene id"):
geneID = allProps["entrez gene id"]
if allProps.has_key("ensembl gene id"):
ensemblID = allProps["ensembl gene id"]
if allProps.has_key("official gene symbol"):
geneSymbol = allProps["official gene symbol"]
if allProps.has_key("5' start"):
fp_start = allProps["5' start"]
if allProps.has_key("3' stop"):
tp_stop = allProps["3' stop"]
if allProps.has_key("5' linker"):
fwd_linker = allProps["5' linker"]
if allProps.has_key("3' linker"):
rev_linker = allProps["3' linker"]
if allProps.has_key("description"):
funcDescr = allProps["description"]
if allProps.has_key("verification"):
verification = allProps["verification"]
if allProps.has_key("comments"):
expComm = allProps["comments"]
if allProps.has_key("verification comments"):
verComm = allProps["verification comments"]
if allProps.has_key("sequence"):
sequence = allProps["sequence"]
# associations
ipvID = ""
senseOligoID = ""
antisenseOligoID = ""
allAssoc = reagent.getAssociations()
'''
if allAssoc.has_key("insert_parent_vector"):
ipvID = allAssoc["insert_parent_vector"]
if allAssoc.has_key("sense_oligo"):
senseOligoID = allAssoc["sense_oligo"]
if allAssoc.has_key("antisense_oligo"):
antisenseOligoID = allAssoc["antisense_oligo"]
'''
# Action: Output form with POST values if set
if cmd == 'create':
content += '''
<div class="main">
<form NAME="create_insert_form" ACTION="%s" METHOD="POST" onSubmit="return validateInsert() && verifyParents();">
'''
content += "<INPUT type=\"hidden\" ID=\"curr_username_hidden\" NAME=\"curr_username\" value=\"" + currUser.getFullName(
) + "\">"
content += '''
<input type="hidden" name="reagent_type_hidden" value="Insert">
<table id="vector_insertproperty_table_id" border="1" width="780px" cellpadding="4" frame="box" rules="all">
'''
if errMsg != "":
content += "<th colspan=\"3\" style=\"color:#0000FF; text-align:left; font-weight:normal\">There was a problem:<br><P>" + errMsg + "<BR><BR></th>"
content += '''
<tr>
<td colspan="3" style="text-align:center">
<span style="color:#0000CD; font-size:13pt; font-weight:bold">
Insert Information
</span>
<br>
<span style="font-size:8pt; color:#FF0000">
Fields marked with a red asterisk (*) are mandatory
</span>
</td>
</tr>
<tr>
<td width="180px">
Type of Insert
<span style="font-size:8pt; color:#FF0000; font-weight:bold">*</span>
</td>
<td width="275px">
<SELECT id="itype_list" size="1" NAME="INPUT_INSERT_info_insert_type_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(iType) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for it in iTypeList:
content += "<OPTION VALUE=\"" + it + "\""
if it == iType:
content += " SELECTED>" + it + "</OPTION>"
else:
content += ">" + it + "</OPTION>"
content += '''
</SELECT>
</td>
<td>
Describes the type of insert. Users select from a pre-defined list. Designed to make insert use more apparent and searches easier.
</td>
</tr>
<tr>
<td>
Name
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_name_prop\" value=\"" + iName + "\">"
content += '''
</td>
<td>
Name that describes the reagent - free text field
</td>
</tr>
<tr>
<td>
Status
</td>
<td>
<SELECT id="status_list" name="INPUT_INSERT_info_status_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(iStatus) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for s in statusList:
content += "<OPTION VALUE=\"" + s + "\""
if s == iStatus:
content += " SELECTED>" + s + "</OPTION>"
else:
content += ">" + s + "</OPTION>"
content += '''
</td>
<td>
Indicates the status and availability of the reagent. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Insert Cloning Method
</td>
<td>
<SELECT size="1" id="cm_list" name="INPUT_INSERT_info_cloning_method_prop" onChange="showCMText()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(cloningMethod) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for cm in cloningMethodList:
content += "<OPTION VALUE=\"" + cm + "\""
if cm == cloningMethod:
content += " SELECTED>" + cm + "</OPTION>"
else:
content += ">" + cm + "</OPTION>"
content += '''
</td>
<td>
Describes the method used to create the insert (e.g. PCR or RE (restriction enzyme)) and provides additional information for its cloning into a vector (eg. by RE, In Fusion or BP reaction)
</td>
</tr>
<tr>
<td>
Project ID <span style="font-size:8pt; color:#FF0000; font-weight:bold">*</span>
</td>
<td>
<select id="packetList_insert" size="1" name="INPUT_INSERT_info_packet_id_prop">
'''
# need to sort projects
pNums = []
projects = {} # (pID, Packet)
for p in projectList:
pID = p.getNumber()
pNums.append(pID)
projects[pID] = p
pNums.sort()
for pID in pNums:
p = projects[pID]
content += "<OPTION VALUE=\"" + ` p.getNumber() ` + "\""
if p.getNumber() == projectID:
content += " SELECTED>" + ` p.getNumber(
) ` + ": " + p.getOwner().getLastName(
) + ": " + p.getName() + "</OPTION>"
else:
content += ">" + ` p.getNumber() ` + ": " + p.getOwner(
).getLastName() + ": " + p.getName() + "</OPTION>"
content += '''
</select>
<BR>
<div id="packet_warning_insert" style="display:none; color:#FF0000">Please select a Project ID from the dropdown list</div>
</td>
<td>
Indicates what person and project originally created the reagent.
</td>
</tr>
<tr>
<td>
5' Cloning Site on Insert
</td>
<td>
<SELECT size="1" id="fpcs_list" name="INPUT_INSERT_info_5_prime_cloning_site_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(fpcs) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for fps in fpcsList:
content += "<OPTION VALUE=\"" + fps + "\""
if fps == fpcs:
content += " SELECTED>" + fps + "</OPTION>"
else:
content += ">" + fps + "</OPTION>"
content += '''
</td>
<td>
Indicates what 5' site on the insert was used to clone it into a vector. May not necessarily be the same as for the vector. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
3' Cloning Site on Insert
</td>
<td>
<SELECT size="1" id="tpcs_list" name="INPUT_INSERT_info_3_prime_cloning_site_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tpcs) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tps in tpcsList:
content += "<OPTION VALUE=\"" + tps + "\""
if tps == tpcs:
content += " SELECTED>" + tps + "</OPTION>"
else:
content += ">" + tps + "</OPTION>"
content += '''
</td>
<td>
Indicates what 3' site on the insert was used to clone it into a vector. May not necessarily be the same as for the vector. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Tag
</td>
<td>
<SELECT size="1" id="tag_list" name="INPUT_INSERT_info_tag_prop" onChange="showTagTypeBox()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tagType) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tt in tagTypeList:
content += "<OPTION VALUE=\"" + tt + "\""
if tt == tagType:
content += " SELECTED>" + tt + "</OPTION>"
else:
content += ">" + tt + "</OPTION>"
content += '''
</td>
<td>
Indicates if the insert itself has a tag associated with it (outside of the backbone vector). Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Tag Position
</td>
<td>
<SELECT size="1" name="INPUT_INSERT_info_tag_position_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tagPosition) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tp in tagPositionList:
content += "<OPTION VALUE=\"" + tp + "\""
if tp == tagPosition:
content += " SELECTED>" + tp + "</OPTION>"
else:
content += ">" + tp + "</OPTION>"
content += '''
</td>
<td>
Describes the position of the tag on the insert. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Open/Closed
</td>
<td>
<SELECT id="oc_list" size="1" name="INPUT_INSERT_info_open_closed_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(openClosed) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for oc in openClosedList:
content += "<OPTION VALUE=\"" + oc + "\""
if oc == openClosed:
content += " SELECTED>" + oc + "</OPTION>"
else:
content += ">" + oc + "</OPTION>"
content += '''
</td>
<td>
Indicates for an Open Reading Frame if there is a start codon (ATG) or stop codon (open - no stop codon, closed - stop codon).
</td>
</tr>
<tr>
<td>
Species
</td>
<td>
<SELECT size="1" style="color:000000" id = "species_list" name="INPUT_INSERT_info_species_prop" onChange="showSpeciesBox()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(species) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for sp in speciesList:
content += "<OPTION VALUE=\"" + sp + "\""
if sp == species:
content += " SELECTED>" + sp + "</OPTION>"
else:
content += ">" + sp + "</OPTION>"
content += '''
</td>
<td>
Indicates the species from which the Insert was derived. User selects species from a pre-defined list.
</td>
</tr>
<tr>
<td>
Accession Number
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_accession_number_prop\" value=\"" + accession + "\">"
content += '''
</td>
<td>
The Accession Number from which the insert was cloned or to which the sequence maps.
</td>
</tr>
<tr>
<td>
Alternate ID
</td>
<td>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="IMAGE" id="_alternate_id_IMAGE_checkbox" onClick="showAltIDTextBox('_alternate_id_IMAGE_checkbox', '_alternate_id_IMAGE_textbox')">IMAGE <INPUT style="display:none" id="_alternate_id_IMAGE_textbox" name="alternate_id_IMAGE_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="RIKEN" id="_alternate_id_RIKEN_checkbox" onClick="showAltIDTextBox('_alternate_id_RIKEN_checkbox', '_alternate_id_RIKEN_textbox')">RIKEN <INPUT style="display:none" id="_alternate_id_RIKEN_textbox" name="alternate_id_RIKEN_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="Kazusa" id="_alternate_id_Kazusa_checkbox" onClick="showAltIDTextBox('_alternate_id_Kazusa_checkbox', '_alternate_id_Kazusa_textbox')">Kazusa <INPUT style="display:none" id="_alternate_id_Kazusa_textbox" name="alternate_id_Kazusa_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="LIFESEQ" id="_alternate_id_LIFESEQ_checkbox" onClick="showAltIDTextBox('_alternate_id_LIFESEQ_checkbox', '_alternate_id_LIFESEQ_textbox')">LIFESEQ <INPUT style="display:none" id="_alternate_id_LIFESEQ_textbox" name="alternate_id_LIFESEQ_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="RZPD" id="_alternate_id_RZPD_checkbox" onClick="showAltIDTextBox('_alternate_id_RZPD_checkbox', '_alternate_id_RZPD_textbox')">RZPD <INPUT style="display:none" id="_alternate_id_RZPD_textbox" name="alternate_id_RZPD_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="HIP" id="_alternate_id_HIP_checkbox" onClick="showAltIDTextBox('_alternate_id_HIP_checkbox', '_alternate_id_HIP_textbox')">HIP <INPUT style="display:none" id="_alternate_id_HIP_textbox" name="alternate_id_HIP_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="ADDGENE" id="_alternate_id_ADDGENE_checkbox" onClick="showAltIDTextBox('_alternate_id_ADDGENE_checkbox', '_alternate_id_ADDGENE_textbox')">ADDGENE <INPUT style="display:none" id="_alternate_id_ADDGENE_textbox" name="alternate_id_ADDGENE_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="PMID" id="_alternate_id_PMID_checkbox" onClick="showAltIDTextBox('_alternate_id_PMID_checkbox', '_alternate_id_PMID_textbox')">PMID <INPUT style="display:none" id="_alternate_id_PMID_textbox" name="alternate_id_PMID_textbox_name" size="15"></INPUT><br>
<input type="checkbox" id="_other_Alt_ID_chkbx" name="INPUT_INSERT_info_alternate_id_prop[]" value="Other" onClick="showSpecificOtherCheckbox('_alternate_id_txt')">Other: <INPUT style="display:none" id="_alternate_id_txt" name="alternate_id_name_txt" size="15"></INPUT>
</td>
<td>
Indicates any other ID's that identify the insert, including but not limited to IMAGE, Kazusa, RIKEN, and other. <BR><BR><BR><BR>For 'Other', please enter the source name and ID separated by a semicolon (e.g. IMAGE:123456)
</td>
</tr>
<tr>
<td>
Entrez Gene ID
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_gene_id_prop\" value=\"" + geneID + "\">"
content += '''
</td>
<td>
The NCBI Gene ID to which the sequence maps.
</td>
</tr>
<tr>
<td>
Ensembl Gene ID
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_ensembl_gene_id_prop\" value=\"" + ensemblID + "\">"
content += '''
</td>
<td>
The Ensembl Gene ID to which the sequence maps.
</td>
</tr>
<tr>
<td>
Official Gene Symbol
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_gene_symbol_prop\" value=\"" + geneSymbol + "\">"
content += '''
</td>
<td>
The official gene symbol for this Insert.
</td>
</tr>
<tr>
<td>
5' Start
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_5_prime_start_prop\" value=\"" + fp_start + "\">"
content += '''
</td>
<td>
Users can map the start of the sequence onto its accession number by indicating at what nucleotide position on the accession number that the sequence starts.
</td>
</tr>
<tr>
<td>
3' Stop
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_3_prime_stop_prop\" value=\"" + tp_stop + "\">"
content += '''
</td>
<td>
Users can map the stop of the sequence onto its accession number by indicating at what nucleotide position on the accession number that the sequence stops
</td>
</tr>
<tr>
<td>
5' Linker
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_5_prime_linker_prop\" value=\"" + fwd_linker + "\">"
content += '''
</td>
<td>
Indicates any sequence added to the 5' end of an insert that does not map to a cDNA sequence but should be included as part of the insert - eg kozak sequences, any nucleotides added to maintain frame.
</td>
</tr>
<tr>
<td>
3' Linker
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_3_prime_linker_prop\" value=\"" + rev_linker + "\">"
content += '''
</td>
<td>
Indicates any sequence added to the 3' end of an insert that does not map to a cDNA sequence but should be included as part of the insert - eg any nucleotides added to maintain frame.
</td>
</tr>
<tr>
<td>
Functional Description
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_description_prop\" value=\"" + funcDescr + "\">"
content += '''
</td>
<td>
Describes the purpose of the reagent and any information that may be key to working with the reagent.
</td>
</tr>
<tr>
<td>
Verification
</td>
<td>
<select size="1" name="INPUT_INSERT_info_verification_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(verification) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for v in verificationList:
content += "<OPTION VALUE=\"" + v + "\""
if v == verification:
content += " SELECTED>" + v + "</OPTION>"
else:
content += ">" + v + "</OPTION>"
content += '''
</select>
</td>
<td>
Indicates if the reagent has been verified and how. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Verification comments
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_verification_comments_prop\" value=\"" + verComm + "\">"
content += '''
</td>
<td>
Allows user to provide a description of the verification status - eg comments on sequence changes, expression levels.
</td>
</tr>
<tr>
<td>
Experimental comments
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_comments_prop\" value=\"" + expComm + "\">"
content += '''
</td>
<td>
Used to describe any information that descrbes how the reagent works in the experimental context - eg low expression, difficult to grow, etc.
</td>
</tr>
<tr>
<td>
Sequence
</td>
<td>
</td>
<td>
The sequence of the insert that corresponds to a cDNA or fragment of interest. Does include artificial start and stop codons. Does not include linker sequences as described above.
</td>
</tr>
<tr>
<td colspan="3">
<textarea rows="10" cols="93" id="dna_sequence" name="INPUT_INSERT_info_sequence_prop">
'''
content += sequence
content += '''
</textarea>
</td>
</tr>
'''
content += self.printParents('Insert', allAssoc)
content += '''
<tr>
<td colspan="3">
<hr><br>
<input type="submit" name="create_reagent" value="Create" onclick="document.pressed = this.value">
</td>
</tr>
</table>
</form>
</div>
'''
# Common to all
content += gOut.printFooter()
page_content = content % (hostname + "cgi/create.py")
print "Content-type:text/html" # THIS IS PERMANENT; DO NOT REMOVE
print # DITTO
print page_content
