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from __future__ import print_function, division, absolute_import
"""
Results will be returned for each of several trait types: mRNA assays, phenotypes, genotypes, and
(maybe later) genes
For each trait type, the results for each species should be given; for example, have a "Mouse" tab
with the mouse traits in a table inside it
This table will then list each trait, its dataset, and several columns determined by its trait type
(phenotype, genotype, etc)
"""
import sys
sys.path.append("../../..")
import simplejson as json
import sqlalchemy as sa
from sqlalchemy.dialects import mysql
from sqlalchemy.orm import scoped_session, sessionmaker, relationship, backref
from sqlalchemy.orm.exc import NoResultFound
from sqlalchemy.ext.declarative import declarative_base
from BeautifulSoup import UnicodeDammit
import zach_settings as settings
Engine = sa.create_engine(settings.SQLALCHEMY_DATABASE_URI,
#encoding='utf-8',
#client_encoding='utf-8',
#echo="debug",
)
Session = scoped_session(sessionmaker(bind=Engine)) #, extension=VersionedListener()))
#Xsession = Session()
Base = declarative_base(bind=Engine)
Metadata = sa.MetaData()
Metadata.bind = Engine
class ProbeSet(Base):
__tablename__ = 'ProbeSet'
__table_args__ = {'autoload': True}
QuickSearch = sa.Table("QuickSearch", Metadata,
sa.Column('table_name', sa.String(15),
primary_key=True, nullable=False, autoincrement=False), # table that item is inserted from
sa.Column('the_key', sa.String(30),
primary_key=True, nullable=False, autoincrement=False), # key in database table
sa.Column('terms', sa.Text), # terms to compare search string with
sa.Column('species', sa.Text),
sa.Column('result_fields', sa.Text) # json
)
#QuickSearch.drop(Engine, checkfirst=True)
Metadata.create_all(Engine)
#class QuickSearch(Base):
# table_name = Column(String)
# the_key = Column(String)
# terms = Column(String)
#
# def __init__(self, table_name, the_key, terms, category, species, result_fields):
# self.table_name = table_name
# self.the_key = the_key
# self.terms = terms
# self.species = species
# self.category = category
# self.result_fields = json.dumps(sort_keys=True)
def get_unique_terms(*args):
if not args:
return None
unique = set()
for item in args:
#print("locals:", locals())
if not item:
continue
for token in item.split():
if token.startswith(('(','[')):
token = token[1:]
if token.endswith((')', ']')):
token = token[:-1]
if token.endswith(';'):
token = token[:-1]
if len(token) > 2:
try:
# This hopefully ensures that the token is utf-8
token = token.encode('utf-8')
print(" ->", token)
except UnicodeDecodeError:
print("\n-- UDE \n")
# Can't get it into utf-8, we won't use it
continue
unique.add(token)
print("\nUnique terms are: {}\n".format(unique))
return " ".join(unique)
def main():
conn = Engine.connect()
counter = 0
for ps in page_query(Session.query(ProbeSet)): #all()
values = {}
values['table_name'] = "ProbeSet"
values['the_key'] = ps.Id
values['terms'] = get_unique_terms(ps.Name, ps.Symbol, ps.description, ps.alias)
print("terms is:", values['terms'])
values['species'] = get_species("ProbeSet", ps.Id)
values['result_fields'] = get_result_fields("ProbeSet", ps.Id)
ins = QuickSearch.insert().values(**values)
conn.execute(ins)
counter += 1
print("Done:", counter)
def get_species(trait_type, trait_id):
if trait_type == "ProbeSet":
print("Before species query")
results = Session.query("Name").from_statement("SELECT Species.Name "
"FROM ProbeSetXRef, "
"ProbeSetFreeze, "
"ProbeFreeze, "
"InbredSet, "
"Species "
"WHERE ProbeSetXRef.ProbeSetId =:probeset_id and "
"ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and "
"ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and "
"ProbeFreeze.InbredSetId = InbredSet.Id and "
"InbredSet.SpeciesId = Species.Id").params(probeset_id=trait_id).all()
print("After query")
assert len(set([result.Name for result in results])) == 1, "Multiple names?"
print("species is:", results[0].Name)
return results[0].Name
def get_result_fields(trait_type, trait_id):
if trait_type == "ProbeSet":
print("qs1")
results = Session.query(
"name", "symbol", "description", "chr", "mb"
).from_statement(
"SELECT ProbeSet.Name as name, "
"ProbeSet.Symbol as symbol, "
"ProbeSet.description as description, "
"ProbeSet.Chr as chr, "
"ProbeSet.Mb as mb "
"FROM ProbeSet "
"WHERE ProbeSet.Id = :probeset_id ").params(probeset_id=trait_id).all()
print("qs2")
for result in results:
print(result)
assert len(set(result for result in results)) == 1, "Different results"
print("results are:", results)
result = results[0]
result = row2dict(result)
try:
json_results = json.dumps(result, sort_keys=True)
except UnicodeDecodeError:
print("\n\nTrying to massage unicode\n\n")
#print("result.__dict__ is [{}]: {}".format(type(result.__dict__), result.__dict__))
#resultd = dict(**result.__dict__)
for key, value in result.iteritems():
print(" key is:", key)
print(" value is:", value)
if isinstance(value, basestring):
result[key] = value.decode('utf-8', errors='ignore')
json_results = json.dumps(result, sort_keys=True)
#print("json is: ", json_results)
return json_results
def row2dict(row):
return dict(zip(row.keys(), row)) # http://stackoverflow.com/a/2848519/1175849
#"""http://stackoverflow.com/a/1960546/1175849"""
#d = {}
#for column in row.__table__.columns:
# d[column.name] = getattr(row, column.name)
#
#return d
def page_query(q):
"""http://stackoverflow.com/a/1217947/1175849"""
offset = 0
while True:
r = False
for elem in q.limit(1000).offset(offset):
r = True
yield elem
offset += 1000
if not r:
break
if __name__ == "__main__":
main()
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