def getModelByMGIIDSubQuery(modelClass, mgiid, mgitypeKeyAttr='_mgitype_key'):
"""
Class must have _mgitype_key class attribute
returns a subquery that can be filter as an exists clause
E.g.
subQuery = getModelByMGIIDSubQuery(Marker, 'MGI:12345')
marker = Marker.query.filter( subQuery.exists() ).first()
"""
sub_model = db.aliased(modelClass)
accession_model = db.aliased(Accession)
# get primary_key name
pkName = class_mapper(modelClass).primary_key[0].name
# get the _mgitype_key
_mgitype_key = getattr(modelClass, mgitypeKeyAttr)
sq = db.session.query(sub_model)
sq = sq.join(accession_model,
db.and_(
accession_model.preferred==1,
accession_model._logicaldb_key==1,
accession_model.prefixpart=='MGI:',
accession_model._object_key==getattr(sub_model, pkName),
accession_model._mgitype_key==_mgitype_key
))
sq = sq.filter(accession_model.accid==mgiid)
sq = sq.filter(getattr(sub_model, pkName)==getattr(modelClass, pkName))
sq = sq.correlate(modelClass)
return sq
def getModelByMGIIDSubQuery(modelClass, mgiid, mgitypeKeyAttr='_mgitype_key'):
"""
Class must have _mgitype_key class attribute
returns a subquery that can be filter as an exists clause
E.g.
subQuery = getModelByMGIIDSubQuery(Marker, 'MGI:12345')
marker = Marker.query.filter( subQuery.exists() ).first()
"""
sub_model = db.aliased(modelClass)
accession_model = db.aliased(Accession)
# get primary_key name
pkName = class_mapper(modelClass).primary_key[0].name
# get the _mgitype_key
_mgitype_key = getattr(modelClass, mgitypeKeyAttr)
sq = db.session.query(sub_model)
sq = sq.join(
accession_model,
db.and_(accession_model.preferred == 1,
accession_model._logicaldb_key == 1,
accession_model.prefixpart == 'MGI:',
accession_model._object_key == getattr(sub_model, pkName),
accession_model._mgitype_key == _mgitype_key))
sq = sq.filter(accession_model.accid == mgiid)
sq = sq.filter(getattr(sub_model, pkName) == getattr(modelClass, pkName))
sq = sq.correlate(modelClass)
return sq
def getAccessionByAccID(id, inMGITypeKeys=[]):
# split and prep the IDs
accidsToSearch = splitCommaInput(id.lower())
# build accid query
query = Accession.query
query = query.filter(
db.and_(
db.func.lower(Accession.accid).in_((accidsToSearch)),
Accession._logicaldb_key.in_((ACCEPTED_LDBS))))
# add keys to filter, if have have any
if inMGITypeKeys:
query = query.filter(Accession._mgitype_key.in_(inMGITypeKeys))
# setting sort
query = query.order_by(Accession._mgitype_key)
#gather accession objects
return query.all()
def getAccessionByAccID(id, inMGITypeKeys=[]):
# split and prep the IDs
accidsToSearch = splitCommaInput(id.lower())
# build accid query
query = Accession.query
query = query.filter(
db.and_(
db.func.lower(Accession.accid).in_((accidsToSearch)),
Accession._logicaldb_key.in_((ACCEPTED_LDBS))
)
)
# add keys to filter, if have have any
if inMGITypeKeys:
query = query.filter(Accession._mgitype_key.in_(inMGITypeKeys))
# setting sort
query = query.order_by(Accession._mgitype_key)
#gather accession objects
return query.all()
