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 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 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 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 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