def createBackbone(self, name, BBtype, desc, seqBefore, seqAfter,
features):
"""Create a BackboneDB and add it to the database.
PARAMETERS:
name: string name of the backbone
BBtype: string type of the backbone; is either "i" for integrative or
"r" for replicative
desc: string description of the backbone
seqBefore: string sequence of the backbone before the insertion region
seqAfter: string sequence of the backbone after the insertion region
features: string features, formatted as it should appear in a .gb file
RETURNS:
bb: created BackboneDB
RAISES:
AlreadyExistsError: if a backbone with the same name is already in
the user's library
"""
#type checking
if (type(name) != str):
raise TypeError("backbone name not a string")
if (type(BBtype) != str):
raise TypeError("backbone type not a string")
elif (BBtype not in ["i", "r"]):
raise ValueError("backbone type not valid")
if (type(desc) != str):
raise TypeError("backbone desc not a string")
if (type(seqBefore) != str):
raise TypeError("backbone seqBefore not a string")
if (type(seqAfter) != str):
raise TypeError("backbone seqAfter not a string")
if (type(features) != str):
raise TypeError("backbone features not a string")
print("done with the type checking")
#see if it exists already
try:
self.findBackbone(name)
raise e.AlreadyExistsError(
"Backbone {name} already exists.".format(name=name))
except e.BackboneNotFoundError:
pass
#create in database
bb = BackboneDB(name=name,
type=BBtype,
desc=desc,
seqBefore=seqBefore,
seqAfter=seqAfter,
features=features,
user_id=self.getID())
db.session.add(bb)
db.session.commit()
return bb
def addNSDB(self, namedSeq):
"""Create a copy of a NamedSequenceDB in the user's library.
PARAMETER:
namedSeq: NamedSequenceDB to copy
RAISES:
AlreadyExistsError: if a named sequence of the same name is already
in the user's library
"""
#type checking
if (type(namedSeq) != NamedSequenceDB):
raise TypeError("namedSeq not a NamedSequenceDB.")
#check if it already exists
try:
self.findNamedSequence(namedSeq.getType(), namedSeq.getName(),
namedSeq.getSeq())
#raise error if it exists
raise e.AlreadyExistsError("Sequence already exists.")
except e.SequenceNotFoundError:
pass
#get info. about namedSeq
NStype = namedSeq.getType()
NSname = namedSeq.getName()
NSseq = namedSeq.getSeq()
nameID = namedSeq.getNameID(
) #####<----- What if, somehow, that NameID already exists in the personal library?
#create a new NamedSequenceDB using the information from namedSeq
#the only difference is the user_id
ns = NamedSequenceDB(elemType=NStype,
name=NSname,
seq=NSseq,
nameID=nameID,
user_id=self.getID())
#add to database
db.session.add(ns)
db.session.commit()
#increment NS id
self.getEntry().incrementID(NStype)
return ns
def addNS(self, namedSeq):
"""Add a NamedSequenceDB to the database using a NamedSequence.
PARAMETERS:
namedSeq: NamedSequence to make a NamedSequenceDB from
RAISES:
AlreadyExistsError: if a NamedSequenceDB with the same name and type
already exists in the database for the user
"""
#type checking
if (type(namedSeq) != NamedSequence):
raise TypeError("namedSeq not a NamedSequence.")
#check if it already exists
try:
self.findNamedSequenceNoSeq(namedSeq.getType(), namedSeq.getName())
#an error will be raised if it exists
raise e.AlreadyExistsError("Sequence already exists.")
except e.SequenceNotFoundError:
pass
#make entry
NStype = namedSeq.getType()
NSname = namedSeq.getName()
NSseq = namedSeq.getSeq()
nameID = self.getEntry().getNextNSid()[NStype]
ns = NamedSequenceDB(elemType=NStype,
name=NSname,
seq=NSseq,
nameID=nameID,
user_id=self.getID())
#add to database
db.session.add(ns)
db.session.commit()
#increment NS id
self.getEntry().incrementID(NStype)
return ns
def new(cls, email):
"""Create a new user: creates a UserData and a UserDataDB.
PARAMTERS:
email: string email of the user
RETURN:
newUserData: created UserData
"""
printIf("Calling UserData.new({email}).\n".format(email=email))
#type validation
if (type(email) != str):
raise TypeError("email not a str")
#see if a user with the email already exists
if (UserDataDB.query.filter_by(email=email).all() != []):
raise e.AlreadyExistsError(
"User with email {email} already exists.".format(email=email))
#initialize
newUserData = cls()
#start nextNSid (the first number for the IDs of named sequences of the user)
if (email == "default"):
nextNSid = 1
else:
nextNSid = 101
#add user to database
u = UserDataDB(nextNSidPR=nextNSid,
nextNSidRBS=nextNSid,
nextNSidGOI=nextNSid,
nextNSidTERM=nextNSid,
email=email)
db.session.add(u)
db.session.commit()
#add database info. to the user
newUserData.__DBid = u.id
newUserData.__entryDB = u
return newUserData
def finishComponent():
"""Create a component and add it to the current user's library."""
#validation
validInput = getAllSelected()
succeeded = False
newID = -1
outputStr = ""
if(validInput):
try:
#get info. to use later
currUser = getCurrUser()
selectedNS = getSelectedNS()
#get spacers & primers, which were stored in the session in JSON
#format, so they need to be re-created using fromJSON()
selectedSpacers = SpacerData.fromJSON(getSelectedSD())
selectedPrimers = PrimerData.fromJSON(getSelectedPD())
#check if it already exists in defaults
try:
defaultUser.findComponent(selectedNS.getType(),
selectedNS.getName(),
selectedSpacers.getPosition(),
selectedSpacers.getTerminalLetter())
#if no error has been raised, the component was found in default
raise ee.AlreadyExistsError("Component already exists as a default component.")
except (ee.SequenceNotFoundError, ee.ComponentNotFoundError):
#the component was not found in default
pass
#check if it already exists in personal library
try:
getCurrUser().findComponent(selectedNS.getType(),
selectedNS.getName(),
selectedSpacers.getPosition(),
selectedSpacers.getTerminalLetter())
#if no error has been raised, the component was found in the
#current user's library.
raise ee.AlreadyExistsError("Component already exists as a user-made component.")
except (ee.SequenceNotFoundError, ee.ComponentNotFoundError):
#the component was not found in the current user
pass
#add NS to personal library if it's not from the personal library
try:
tempNS = currUser.addNSDB(selectedNS)
selectedNS = tempNS
except ee.AlreadyExistsError:
pass
#create the component
newComponent = currUser.createComp(selectedNS, selectedSpacers, selectedPrimers)
#modify output string
libraryName = "Personal"
outputStr = ("<a target = '_blank' href = '/library#{libraryName}{nameID}'>"
"{nameID}</a> created.").format(
libraryName = libraryName,
nameID = newComponent.getNameID())
#get the ID of the new component, for the ZIP download link/button
newID = newComponent.getID()
succeeded = True
except Exception as e:
outputStr = "ERROR: " + str(e)
else:
outputStr += "ERROR: invalid input."
return jsonify({"output": outputStr, "succeeded": succeeded, "newID": newID})
def createComp(self, NSentry, spacerData, primerData):
"""Make a ComponentDB and add to the database using a NamedSequenceDB in the
database, a SpacerData, and a PrimerData.
PARAMETERS:
NSentry: NamedSequenceDB in the database that the component will use
spacerData: SpacerData for the component
primerData: PrimerData for the component
RETURNS:
c: created ComponentDB that is now in the database.
"""
#type checking
if (type(NSentry) != NamedSequenceDB):
raise TypeError("NSentry not a NamedSequenceDB")
if (type(spacerData) != SpacerData):
raise TypeError("spacerData not a SpacerData")
if (type(primerData) != PrimerData):
raise TypeError("primerData not a PrimerData")
#check if the component already exists
try:
self.findComponent(NSentry.getType(), NSentry.getName(),
spacerData.getPosition(),
spacerData.getTerminalLetter())
raise e.AlreadyExistsError("Component already exists.")
except e.ComponentNotFoundError:
pass
#create database entries
s = SpacerDataDB(position=spacerData.getPosition(),
spacerLeft=spacerData.getSpacerLeft(),
spacerRight=spacerData.getSpacerRight(),
isTerminal=spacerData.getIsTerminal(),
terminalLetter=spacerData.getTerminalLetter(),
leftNN=spacerData.getLeftNN(),
rightNN=spacerData.getRightNN())
p = PrimerDataDB(primersFound=primerData.getPrimersFound(),
seqLeft=primerData.getLeftSeq(),
seqRight=primerData.getRightSeq(),
GCleft=primerData.getGCleft(),
GCright=primerData.getGCright(),
TMleft=primerData.getTMleft(),
TMright=primerData.getTMright())
c = ComponentDB(namedSequence_id=NSentry.getID(), user_id=self.getID())
#add to the database
db.session.add(c)
db.session.add(s)
db.session.add(p)
db.session.commit()
#edit database entries so they have proper relations
c.setSpacerDataID(s.getID())
c.setPrimerDataID(p.getID())
s.setCompID(c.getID())
p.setCompID(c.getID())
db.session.commit()
return c