aboutsummaryrefslogtreecommitdiff
path: root/wqflask/maintenance
diff options
context:
space:
mode:
authorLei Yan2013-06-19 21:08:43 +0000
committerLei Yan2013-06-19 21:08:43 +0000
commit0dd5dfb3925b2198487480d6093eed0d92201fc6 (patch)
treecc103e4067d42442b0d86602f104a406d172945d /wqflask/maintenance
parent71f1a5d52d58d07294ef3f2cfa87026025358e74 (diff)
parentaac1dd2f9c5b216b24c6e35676ba5d50f9d5d3c2 (diff)
downloadgenenetwork2-0dd5dfb3925b2198487480d6093eed0d92201fc6.tar.gz
Merge branch 'flask' of git://github.com/zsloan/genenetwork into flask
Conflicts: wqflask/base/data_set.py
Diffstat (limited to 'wqflask/maintenance')
-rw-r--r--wqflask/maintenance/print_benchmark.py43
-rw-r--r--wqflask/maintenance/quick_search_table.py137
2 files changed, 121 insertions, 59 deletions
diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py
new file mode 100644
index 00000000..540e0904
--- /dev/null
+++ b/wqflask/maintenance/print_benchmark.py
@@ -0,0 +1,43 @@
+#!/usr/bin/python
+
+from __future__ import absolute_import, print_function, division
+
+import time
+
+from pprint import pformat as pf
+
+
+class TheCounter(object):
+ Counters = {}
+
+ def __init__(self):
+ start_time = time.time()
+ for counter in range(170000):
+ self.print_it(counter)
+ self.time_took = time.time() - start_time
+ TheCounter.Counters[self.__class__.__name__] = self.time_took
+
+class PrintAll(TheCounter):
+ def print_it(self, counter):
+ print(counter)
+
+class PrintSome(TheCounter):
+ def print_it(self, counter):
+ if counter % 1000 == 0:
+ print(counter)
+
+class PrintNone(TheCounter):
+ def print_it(self, counter):
+ pass
+
+
+def new_main():
+ print("Running new_main")
+ tests = [PrintAll, PrintSome, PrintNone]
+ for test in tests:
+ test()
+
+ print(pf(TheCounter.Counters))
+
+if __name__ == '__main__':
+ new_main() \ No newline at end of file
diff --git a/wqflask/maintenance/quick_search_table.py b/wqflask/maintenance/quick_search_table.py
index 046a05c4..b07e7656 100644
--- a/wqflask/maintenance/quick_search_table.py
+++ b/wqflask/maintenance/quick_search_table.py
@@ -1,17 +1,17 @@
-from __future__ import print_function, division, absolute_import
+"""Creates a table used for the quick search feature.
+
+One column contains the terms to match the user's search against. Another contains the result
+fields in json format
-"""
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)
+For each trait type, the results for each species should be given This table will then list
+each trait, its dataset, and several columns determined by its trait type (phenotype, genotype, etc)
"""
+from __future__ import print_function, division, absolute_import
import sys
sys.path.append("../../..")
@@ -19,19 +19,17 @@ 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.orm import scoped_session, sessionmaker
from sqlalchemy.ext.declarative import declarative_base
-from pprint import pformat as pf
+#from pprint import pformat as pf
import zach_settings as settings
Engine = sa.create_engine(settings.SQLALCHEMY_DATABASE_URI,
#encoding='utf-8',
#client_encoding='utf-8',
- #echo="debug",
+ #echo="debug",w
)
Session = scoped_session(sessionmaker(bind=Engine)) #, extension=VersionedListener()))
@@ -41,6 +39,14 @@ Metadata = sa.MetaData()
Metadata.bind = Engine
class PublishXRef(Base):
+ """Class that corresponds with the PublishXRef table in the database.
+
+ The PublishXRef table links phenotype traits and their publications.
+
+ This class is used to add phenotype traits to the quick search table.
+
+ """
+
__tablename__ = 'PublishXRef'
Id = sa.Column(sa.Integer, primary_key=True)
@@ -56,15 +62,16 @@ class PublishXRef(Base):
@classmethod
def run(cls):
+ """Connects to database and inserts phenotype trait info into the Quicksearch table."""
conn = Engine.connect()
counter = 0
- for ps in page_query(Session.query(cls)): #all()
+ for pub_row in page_query(Session.query(cls)): #all()
values = {}
values['table_name'] = cls.__tablename__
- values['the_key'] = json.dumps([ps.Id, ps.InbredSetId])
- values['terms'] = cls.get_unique_terms(ps.Id, ps.InbredSetId)
+ values['the_key'] = json.dumps([pub_row.Id, pub_row.InbredSetId])
+ values['terms'] = cls.get_unique_terms(pub_row.Id, pub_row.InbredSetId)
print("terms is:", values['terms'])
- values['result_fields'] = cls.get_result_fields(ps.Id, ps.InbredSetId)
+ values['result_fields'] = cls.get_result_fields(pub_row.Id, pub_row.InbredSetId)
ins = QuickSearch.insert().values(**values)
conn.execute(ins)
counter += 1
@@ -72,6 +79,7 @@ class PublishXRef(Base):
@staticmethod
def get_unique_terms(publishxref_id, inbredset_id):
+ """Finds unique terms for each item in the PublishXRef table to match a query against"""
results = Session.query(
"pre_publication_description",
"post_publication_description",
@@ -119,6 +127,7 @@ class PublishXRef(Base):
@staticmethod
def get_result_fields(publishxref_id, inbredset_id):
+ """Gets the result fields (columns) that appear on the result page as a json string"""
results = Session.query(
"phenotype_id",
"species",
@@ -136,7 +145,7 @@ class PublishXRef(Base):
"Phenotype.Original_description as description, "
"PublishXRef.LRS as lrs, "
"PublishXRef.PublicationId as publication_id, "
- "Publication.PubMed_ID"
+ "Publication.PubMed_ID as pubmed_id, "
"Publication.Year as year, "
"Publication.Authors as authors "
"FROM PublishXRef, "
@@ -150,17 +159,10 @@ class PublishXRef(Base):
"PublishXRef.PublicationId = Publication.Id and "
"InbredSet.Id = :inbredset_id and "
"Species.Id = InbredSet.SpeciesId ").params(publishxref_id=publishxref_id,
- inbredset_id=inbredset_id).all()
- #"InbredSet.SpeciesId = Species.Id and "
- #"Geno.SpeciesId = Species.Id and "
- #"Geno.Name = PublishXRef.Locus ").params(publishxref_id=publishxref_id,
- # inbredset_id=inbredset_id).all()
- #for result in results:
- # print("****", result)
+ inbredset_id=inbredset_id).all()
assert len(set(result for result in results)) == 1, "Different results or no results"
- #print("results are:", results)
result = results[0]
result = row2dict(result)
try:
@@ -176,7 +178,16 @@ class PublishXRef(Base):
return json_results
+
class GenoXRef(Base):
+ """Class that corresponds with the GenoXRef table in the database.
+
+ The GenoXRef table links genotype traits and their data.
+
+ This class is used to add genotype traits to the quick search table.
+
+ """
+
__tablename__ = 'GenoXRef'
GenoFreezeId = sa.Column(sa.Integer, primary_key=True)
@@ -187,6 +198,7 @@ class GenoXRef(Base):
@classmethod
def run(cls):
+ """Connects to database and inserts genotype trait info into the Quicksearch table."""
conn = Engine.connect()
counter = 0
for item in page_query(Session.query(cls)): #all()
@@ -201,9 +213,10 @@ class GenoXRef(Base):
conn.execute(ins)
counter += 1
print("Done:", counter)
-
+
@staticmethod
def get_unique_terms(geno_id):
+ """Finds unique terms for each item in the GenoXRef table to match a query against"""
print("geno_id: ", geno_id)
results = Session.query(
"name",
@@ -214,8 +227,6 @@ class GenoXRef(Base):
"FROM Geno "
"WHERE Geno.Id = :geno_id ").params(geno_id=geno_id).all()
- #print("results: ", pf(results))
-
unique = set()
if len(results):
for item in results[0]:
@@ -234,12 +245,12 @@ class GenoXRef(Base):
continue
unique.add(token)
- #print("\nUnique terms are: {}\n".format(unique))
return " ".join(unique)
@staticmethod
def get_result_fields(geno_id, dataset_id):
+ """Gets the result fields (columns) that appear on the result page as a json string"""
results = Session.query(
"name",
"marker_name",
@@ -271,11 +282,8 @@ class GenoXRef(Base):
"InbredSet.Id = GenoFreeze.InbredSetId and "
"InbredSet.SpeciesId = Species.Id ").params(geno_id=geno_id,
dataset_id=dataset_id).all()
- #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:
@@ -292,6 +300,14 @@ class GenoXRef(Base):
return json_results
class ProbeSetXRef(Base):
+ """Class that corresponds with the ProbeSetXRef table in the database.
+
+ The ProbeSetXRef table links mRNA expression traits and their sample data.
+
+ This class is used to add mRNA expression traits to the quick search table.
+
+ """
+
__tablename__ = 'ProbeSetXRef'
ProbeSetFreezeId = sa.Column(sa.Integer, primary_key=True)
@@ -310,16 +326,17 @@ class ProbeSetXRef(Base):
@classmethod
def run(cls):
+ """Connects to db and inserts mRNA expression trait info into the Quicksearch table."""
conn = Engine.connect()
counter = 0
- for ps in page_query(Session.query(cls)): #all()
+ for ps_row in page_query(Session.query(cls)): #all()
values = {}
values['table_name'] = cls.__tablename__
- values['the_key'] = json.dumps([ps.ProbeSetId, ps.ProbeSetFreezeId])
- values['terms'] = cls.get_unique_terms(ps.ProbeSetId)
+ values['the_key'] = json.dumps([ps_row.ProbeSetId, ps_row.ProbeSetFreezeId])
+ values['terms'] = cls.get_unique_terms(ps_row.ProbeSetId)
print("terms is:", values['terms'])
- #values['species'] = get_species("ProbeSet", ps.Id)
- values['result_fields'] = cls.get_result_fields(ps.ProbeSetId, ps.ProbeSetFreezeId)
+ values['result_fields'] = cls.get_result_fields(ps_row.ProbeSetId,
+ ps_row.ProbeSetFreezeId)
if values['result_fields'] == None:
continue
ins = QuickSearch.insert().values(**values)
@@ -329,6 +346,7 @@ class ProbeSetXRef(Base):
@staticmethod
def get_unique_terms(probeset_id):
+ """Finds unique terms for each item in the ProbeSetXRef table to match a query against"""
results = Session.query(
"name",
"symbol",
@@ -345,7 +363,6 @@ class ProbeSetXRef(Base):
unique = set()
if len(results):
for item in results[0]:
- #print("locals:", locals())
if not item:
continue
for token in item.split():
@@ -366,12 +383,12 @@ class ProbeSetXRef(Base):
continue
unique.add(token)
- #print("\nUnique terms are: {}\n".format(unique))
return " ".join(unique)
@staticmethod
def get_result_fields(probeset_id, dataset_id):
+ """Gets the result fields (columns) that appear on the result page as a json string"""
print("probeset_id: ", probeset_id)
print("dataset_id: ", dataset_id)
results = Session.query(
@@ -420,14 +437,10 @@ class ProbeSetXRef(Base):
"ProbeFreeze.InbredSetId = InbredSet.Id and "
"InbredSet.SpeciesId = Species.Id ").params(probeset_id=probeset_id,
dataset_id=dataset_id).all()
- #for result in results:
- # print("-", result)
if len(set(result for result in results)) != 1:
return None
- #assert len(set(result for result in results)) == 1, "Different results"
-
- #print("results are:", results)
+
result = results[0]
result = row2dict(result)
try:
@@ -443,42 +456,48 @@ class ProbeSetXRef(Base):
return json_results
-
QuickSearch = sa.Table("QuickSearch", Metadata,
+ # table_name is the table that item is inserted from
sa.Column('table_name', sa.String(15),
- primary_key=True, nullable=False, autoincrement=False), # table that item is inserted from
+ primary_key=True, nullable=False, autoincrement=False),
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('result_fields', sa.Text) # json
+ sa.Column('result_fields', sa.Text), # json
+ mysql_engine = 'MyISAM',
)
-QuickSearch.drop(Engine, checkfirst=True)
-Metadata.create_all(Engine)
+#QuickSearch.drop(Engine, checkfirst=True)
+#Metadata.create_all(Engine)
def row2dict(row):
- """http://stackoverflow.com/a/2848519/1175849"""
+ """From http://stackoverflow.com/a/2848519/1175849"""
return dict(zip(row.keys(), row))
-def page_query(q):
- """http://stackoverflow.com/a/1217947/1175849"""
+def page_query(query):
+ """From http://stackoverflow.com/a/1217947/1175849"""
offset = 0
while True:
- r = False
- for elem in q.limit(1000).offset(offset):
- r = True
- yield elem
+ rrr = False
+ for elem in query.limit(1000).offset(offset):
+ rrr = True
+ yield elem
offset += 1000
- if not r:
+ if not rrr:
break
def main():
+ """Populate the QuickSearch table that is used with the quick search features.
+
+ Add all items from the ProbeSetXRef, GenoXRef, and PublishXRef tables to the QuickSearch tables.
+
+ """
ProbeSetXRef.run()
- GenoXRef.run()
- PublishXRef.run()
+ #GenoXRef.run()
+ #PublishXRef.run()
if __name__ == "__main__":
main() \ No newline at end of file