Removing unnecessary closing code

requirements.txt

@@ -21,5 +21,4 @@ voluptuous==0.8.5
 wsgiref==0.1.2
 dpxdt==0.1.5
 psycopg2==2.5.4
-testing.postgresql
 git+git://github.com/hammerlab/pyensembl

tests/python/test.py

@@ -1,11 +1,6 @@
 import nose
-from nose.tools import eq_, ok_
-from sqlalchemy import create_engine
-import testing.postgresql as testpg
-from unittest import TestCase
 
 from cycledash.helpers import underscorize
-from workers.gene_annotator import closing
 from workers.relational_vcfs import vcf_to_csv
 
 
@@ -34,90 +29,3 @@ def test_vcf_to_csv():
     assert rows[0] == ['44', '', '81', 'True']
     assert rows[-1] == ['40', '', '74', 'True']
     assert len(rows) == 20
-
-
-def test_closing_file():
-    file_name = 'tests/js/data/snv.vcf'
-
-    # Without the closing function
-    file = open(file_name)
-    _ok_open(file)
-    with file:
-        pass
-    _ok_closed(file)
-
-    # Using the closing function
-    file = open(file_name)
-    _ok_open(file)
-    with closing(file):
-        pass
-    _ok_closed(file)
-
-
-def test_closing_pre_finally():
-    file = open('tests/js/data/snv.vcf')
-
-    def add_to_dict(d):
-        d[0] = 1
-
-    d = {}
-    ok_(not d, "d should be empty")
-    with closing(file, pre_finally_fun=add_to_dict, d=d):
-        pass
-    eq_(len(d), 1, "d should have one element")
-    _ok_closed(file)
-
-
-class TestClosingDB(TestCase):
-    @classmethod
-    def setUpClass(cls):
-        # TODO(tavi) Make this faster. Perhaps mock it out?
-        cls.pg = testpg.Postgresql()
-        cls.engine = create_engine(cls.pg.url())
-
-    @classmethod
-    def tearDownClass(cls):
-        cls.pg.stop()
-
-    def setUp(self):
-        with testpg.Postgresql() as pg:
-            self.connection = self.engine.connect()
-            self.cursor = self.connection.connection.cursor()
-
-    def tearDown(self):
-        if self.cursor:
-            self.cursor.close()
-        if self.connection:
-            self.connection.close()
-
-    def test_connection_without_closing(self):
-        _ok_open(self.connection)
-        with self.connection:
-            pass
-        _ok_closed(self.connection)
-
-    def test_connection_with_closing(self):
-        _ok_open(self.connection)
-        with closing(self.connection):
-            pass
-        _ok_closed(self.connection)
-
-    def test_cursor_without_closing(self):
-        _ok_open(self.cursor)
-        with self.cursor:
-            pass
-        _ok_closed(self.cursor)
-
-    def test_cursor_with_closing(self):
-        _ok_open(self.cursor)
-        with closing(self.cursor):
-            pass
-        _ok_closed(self.cursor)
-
-
-def _ok_closed(thing):
-    ok_(thing.closed, "The object should have gotten closed")
-
-
-def _ok_open(thing):
-    ok_(not thing.closed, "The object should be open")

workers/gene_annotator.py

@@ -26,10 +26,8 @@
 # TODO(tavi) Handle inconsistent states and retries.
 @worker.task
 def annotate(vcf_id):
-    engine, connection, metadata = initialize_database(DATABASE_URI)
-
-    with closing(connection, pre_finally_fun=discard_temp,
-            connection=connection):
+    _, connection, metadata = initialize_database(DATABASE_URI)
+    try:
         genotypes = metadata.tables.get('genotypes')
         stmt = select([genotypes.c.contig, genotypes.c.position]).where(
             genotypes.c.vcf_id == vcf_id)
@@ -51,16 +49,14 @@ def annotate(vcf_id):
 
         # Open file for both writing (the gene annotations) and reading that
         # out to Postgres
-        csv_file = temp_csv(mode='r+', tmp_dir=TEMPORARY_DIR)
-        with closing(csv_file):
+        with temp_csv(mode='r+', tmp_dir=TEMPORARY_DIR) as csv_file:
             # Don't use commas as a delim, as commas are part of gene_names
             csv.writer(csv_file, delimiter='\t').writerows(gene_names)
 
             # Back to the beginning of the file
             csv_file.seek(0, 0)
 
-            cursor = connection.connection.cursor()
-            with closing(cursor):
+            with connection.connection.cursor() as cursor:
                 tmp_table = Table('gene_annotations',
                     metadata,
                     Column('contig', Text, nullable=False),
@@ -82,20 +78,5 @@ def annotate(vcf_id):
 
                 # Update the list of extant columns for the UI
                 update_extant_columns(metadata, connection, vcf_id)
-
-def discard_temp(**kwargs):
-    connection = kwargs.get('connection', None)
-    if connection:
-        connection.execute("DISCARD TEMP")
-        connection.connection.commit()
-
-@contextmanager
-def closing(thing, pre_finally_fun=None, **kwargs):
-    try:
-        yield thing
     finally:
-        try:
-            if pre_finally_fun:
-                pre_finally_fun(**kwargs)
-        finally:
-            thing.close()
+        connection.execute("DISCARD TEMP")