From 94df7c071a1f8b582b0a960e6abd28e20609b279 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Mon, 23 Dec 2013 00:26:52 +0100
Subject: [PATCH] Fix unit tests with SQLAlchemy
This involves making the SQLAlchemy session reconfigurable at run-time,
which is done automatically on updating the Mutalyzer configuration using
configuration update callbacks.
---
mutalyzer/Scheduler.py | 4 +-
mutalyzer/config/__init__.py | 41 +++++++++++++--
mutalyzer/config/default_settings.py | 3 ++
mutalyzer/db/__init__.py | 67 +++++++++++++++++++-----
mutalyzer/db/models.py | 13 +++++
tests/test_crossmap.py | 9 ++--
tests/test_describe.py | 14 ++---
tests/test_grammar.py | 10 ++--
tests/test_mapping.py | 9 ++--
tests/test_mutator.py | 9 ++--
tests/test_parsers_genbank.py | 9 ++--
tests/test_scheduler.py | 77 +++++++++++++++++++++++++---
tests/test_services_json.py | 9 ++--
tests/test_services_soap.py | 8 ++-
tests/test_variantchecker.py | 9 ++--
tests/test_website.py | 22 ++------
tests/utils.py | 34 +++++++++---
17 files changed, 242 insertions(+), 105 deletions(-)
diff --git a/mutalyzer/Scheduler.py b/mutalyzer/Scheduler.py
index 60ac5711..b675c4b9 100644
--- a/mutalyzer/Scheduler.py
+++ b/mutalyzer/Scheduler.py
@@ -265,10 +265,10 @@ Mutalyzer batch scheduler""" % url)
# NOTE:
# Flags is a list of tuples. Each tuple consists of a flag and its
# arguments. A skipped entry has only one argument, the selector
- # E.g. ("S1", "NM_002001.$")
+ # E.g. ("S1", "NM_002001.")
# An altered entry has three arguments,
# old, new negative selector
- # E.g.("A2",("NM_002001", "NM_002001.2", "NM_002001[[.period.]]"))
+ # E.g.("A2",("NM_002001", "NM_002001.2", "NM_002001."))
# Flags are set when an entry could be sped up. This is either the
# case for the Retriever as for the Mutalyzer module
diff --git a/mutalyzer/config/__init__.py b/mutalyzer/config/__init__.py
index 5617162b..4d8d9940 100644
--- a/mutalyzer/config/__init__.py
+++ b/mutalyzer/config/__init__.py
@@ -6,15 +6,17 @@ module and overridden by any values from the module specified by the
`MUTALYZER_SETTINGS`.
Alternatively, the default values can be overridden manually using the
-:meth:`settings.configure` method before the first use of a configuration
-value, in which case the `MUTALYZER_SETTINGS` environment variable will not be
-used.
+:meth:`settings.configure` method. If this is done before the first use of a
+configuration value, the `MUTALYZER_SETTINGS` environment variable will never
+be used.
"""
-import flask.config
+import collections
import os
+import flask.config
+
from mutalyzer import util
@@ -38,9 +40,19 @@ class LazySettings(util.LazyObject):
Taken from `Django <https://www.djangoproject.com/>`_
(`django.conf.LazySettings`).
+ Configuration settings can be updated with the :meth:`configure` method.
+
+ The user can register callbacks to configuration keys that are called
+ whenever the value for that key is updated with :meth:`on_update`.
+
.. note:: Django also does some logging config magic here, we did not copy
that.
"""
+ def __init__(self, *args, **kwargs):
+ # Assign to __dict__ to avoid __setattr__ call.
+ self.__dict__['_callbacks'] = collections.defaultdict(list)
+ super(LazySettings, self).__init__(*args, **kwargs)
+
def _setup(self, from_environment=True):
"""
Load the settings module pointed to by the environment variable. This
@@ -60,6 +72,16 @@ class LazySettings(util.LazyObject):
self._setup(from_environment=False)
self._wrapped.update(settings)
+ # Callbacks for specific keys.
+ for key, callbacks in self._callbacks.items():
+ if key in settings:
+ for callback in callbacks:
+ callback(settings[key])
+
+ # General callbacks.
+ for callback in self._callbacks[None]:
+ callback(settings)
+
@property
def configured(self):
"""
@@ -67,5 +89,16 @@ class LazySettings(util.LazyObject):
"""
return self._wrapped is not None
+ def on_update(self, callback, key=None):
+ """
+ Register a callback for the update of a key (or any update if `key` is
+ `None`).
+
+ The callback is called with as argument the new value for the updated
+ key (or a dictionary with all updated key-value pairs if `key` is
+ `None`).
+ """
+ self._callbacks[key].append(callback)
+
settings = LazySettings()
diff --git a/mutalyzer/config/default_settings.py b/mutalyzer/config/default_settings.py
index 3d2e33cd..03dd2a10 100644
--- a/mutalyzer/config/default_settings.py
+++ b/mutalyzer/config/default_settings.py
@@ -26,6 +26,9 @@ MAX_CACHE_SIZE = 50 * 1048576 # 50 MB
# Maximum size for uploaded and downloaded files (in bytes).
MAX_FILE_SIZE = 10 * 1048576 # 10 MB
+# Database connection URL (can be any SQLAlchemy connection URI).
+DATABASE_URI = 'sqlite://'
+
# Host name for local MySQL databases.
MYSQL_HOST = 'localhost'
diff --git a/mutalyzer/db/__init__.py b/mutalyzer/db/__init__.py
index 41b6910b..8282e824 100644
--- a/mutalyzer/db/__init__.py
+++ b/mutalyzer/db/__init__.py
@@ -4,27 +4,66 @@ using SQLAlchemy.
"""
-from sqlalchemy import create_engine
+import sqlalchemy
+from sqlalchemy.engine.url import make_url
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy.orm import scoped_session, sessionmaker
+from sqlalchemy.pool import StaticPool
+from mutalyzer.config import settings
-engine = create_engine('sqlite:////tmp/test.db') #, echo=True)
-session_factory = sessionmaker(bind=engine)
+class SessionFactory(sessionmaker):
+ """
+ Session factory that configures the engine lazily at first use with the
+ current settings.DATABASE_URI.
+ """
+ def __call__(self, **local_kw):
+ if self.kw['bind'] is None and 'bind' not in local_kw:
+ self.kw['bind'] = create_engine()
+ return super(SessionFactory, self).__call__(**local_kw)
-session = scoped_session(session_factory)
-Base = declarative_base()
-Base.query = session.query_property()
+def create_engine():
+ """
+ Create an SQLAlchemy connection engine from the current configuration.
+ """
+ url = make_url(settings.DATABASE_URI)
+ options = {}
+
+ if settings.DEBUG:
+ options.update(echo=True)
+
+ if url.drivername == 'sqlite' and url.database in (None, '', ':memory:'):
+ # SQLite in-memory database are created per connection, so we need a
+ # singleton pool if we want to see the same database across threads,
+ # web requests, etcetera.
+ options.update(
+ connect_args={'check_same_thread': False},
+ poolclass=StaticPool)
+
+ return sqlalchemy.create_engine(url, **options)
+
+def configure_session(uri):
+ """
+ (Re)configure the session by closing the existing session if it exists and
+ loading the current configuration for use by future sessions.
+ """
+ global session_factory, session
+ session.remove()
+ session_factory.configure(bind=create_engine())
-def create_database():
- Base.metadata.drop_all(engine)
- Base.metadata.create_all(engine)
- # if using alembic:
- #from alembic.config import Config
- #from alembic import command
- #alembic_cfg = Config("alembic.ini")
- #command.stamp(alembic_cfg, "head")
+# Reconfigure the session if database configuration is updated.
+settings.on_update(configure_session, 'DATABASE_URI')
+
+
+# Session are automatically created where needed and are scoped by thread.
+session_factory = SessionFactory()
+session = scoped_session(session_factory)
+
+
+# Base class to use in our models.
+Base = declarative_base()
+Base.query = session.query_property()
diff --git a/mutalyzer/db/models.py b/mutalyzer/db/models.py
index 93a5f591..c3fc9b4b 100644
--- a/mutalyzer/db/models.py
+++ b/mutalyzer/db/models.py
@@ -118,3 +118,16 @@ class BatchQueueItem(db.Base):
Index('batch_queue_item_with_batch_job',
BatchQueueItem.batch_job_id, BatchQueueItem.id)
+
+
+def create_all():
+ db.Base.metadata.drop_all(db.session.get_bind())
+ db.Base.metadata.create_all(db.session.get_bind())
+
+ # Todo: Use alembic.
+
+ # if using alembic:
+ #from alembic.config import Config
+ #from alembic import command
+ #alembic_cfg = Config("alembic.ini")
+ #command.stamp(alembic_cfg, "head")
diff --git a/tests/test_crossmap.py b/tests/test_crossmap.py
index d0f60411..489e4252 100644
--- a/tests/test_crossmap.py
+++ b/tests/test_crossmap.py
@@ -3,20 +3,21 @@ Tests for the Crossmap module.
"""
-from utils import TEST_SETTINGS
-from mutalyzer.config import settings
-settings.configure(TEST_SETTINGS)
-
#import logging; logging.basicConfig()
from nose.tools import *
from mutalyzer.Crossmap import Crossmap
+import utils
+
class TestCrossmap():
"""
Test the Crossmap class.
"""
+ def setup(self):
+ utils.create_test_environment(database=True)
+
def test_splice_sites(self):
"""
Check whether the gene on the forward strand has the right splice
diff --git a/tests/test_describe.py b/tests/test_describe.py
index d4a3a96c..9974709a 100644
--- a/tests/test_describe.py
+++ b/tests/test_describe.py
@@ -3,10 +3,6 @@ Tests for the mutalyzer.describe module.
"""
-from utils import TEST_SETTINGS
-from mutalyzer.config import settings
-settings.configure(TEST_SETTINGS)
-
#import logging; logging.basicConfig()
import os
from nose.tools import *
@@ -14,17 +10,15 @@ from nose.tools import *
import mutalyzer
from mutalyzer import describe
+import utils
+
class TestDescribe():
"""
Test the mytalyzer.describe module.
"""
-
- def setUp(self):
- """
- Nothing.
- """
- pass
+ def setup(self):
+ utils.create_test_environment()
def test1(self):
"""
diff --git a/tests/test_grammar.py b/tests/test_grammar.py
index 2a20abd5..9abf02d8 100644
--- a/tests/test_grammar.py
+++ b/tests/test_grammar.py
@@ -3,10 +3,6 @@ Tests for the mutalyzer.grammar module.
"""
-from utils import TEST_SETTINGS
-from mutalyzer.config import settings
-settings.configure(TEST_SETTINGS)
-
#import logging; logging.basicConfig()
import os
from nose.tools import *
@@ -15,16 +11,18 @@ import mutalyzer
from mutalyzer.grammar import Grammar
from mutalyzer.output import Output
+import utils
+
class TestGrammar():
"""
Test the mytalyzer.grammar module.
"""
-
- def setUp(self):
+ def setup(self):
"""
Initialize test Grammar instance.
"""
+ utils.create_test_environment()
self.output = Output(__file__)
self.grammar = Grammar(self.output)
diff --git a/tests/test_mapping.py b/tests/test_mapping.py
index 33674e0c..8c4e6c59 100644
--- a/tests/test_mapping.py
+++ b/tests/test_mapping.py
@@ -3,25 +3,24 @@ Tests for the mapping module.
"""
-from utils import TEST_SETTINGS
-from mutalyzer.config import settings
-settings.configure(TEST_SETTINGS)
-
#import logging; logging.basicConfig()
from nose.tools import *
from mutalyzer.output import Output
from mutalyzer.mapping import Converter
+import utils
+
class TestConverter():
"""
Test the Converter class.
"""
- def setUp(self):
+ def setup(self):
"""
Initialize test converter module.
"""
+ utils.create_test_environment(database=True)
self.output = Output(__file__)
def _converter(self, build):
diff --git a/tests/test_mutator.py b/tests/test_mutator.py
index 8b32e8f6..6f8391ce 100644
--- a/tests/test_mutator.py
+++ b/tests/test_mutator.py
@@ -3,10 +3,6 @@ Tests for the mutalyzer.mutator module.
"""
-from utils import TEST_SETTINGS
-from mutalyzer.config import settings
-settings.configure(TEST_SETTINGS)
-
#import logging; logging.basicConfig()
import re
import os
@@ -19,6 +15,8 @@ from mutalyzer.util import skip
from mutalyzer.output import Output
from mutalyzer import mutator
+import utils
+
def _seq(length):
"""
@@ -34,10 +32,11 @@ class TestMutator():
"""
Test the mutator module.
"""
- def setUp(self):
+ def setup(self):
"""
Initialize test mutator module.
"""
+ utils.create_test_environment()
self.output = Output(__file__)
def _mutator(self, sequence):
diff --git a/tests/test_parsers_genbank.py b/tests/test_parsers_genbank.py
index a04aa5fa..a574cfb4 100644
--- a/tests/test_parsers_genbank.py
+++ b/tests/test_parsers_genbank.py
@@ -3,24 +3,23 @@ Tests for the mutalyzer.parsers.genbank module.
"""
-from utils import TEST_SETTINGS
-from mutalyzer.config import settings
-settings.configure(TEST_SETTINGS)
-
#import logging; logging.basicConfig()
from nose.tools import *
from mutalyzer.parsers import genbank
+import utils
+
class TestMutator():
"""
Test the mutator module.
"""
- def setUp(self):
+ def setup(self):
"""
Initialize test mutator module.
"""
+ utils.create_test_environment(database=True)
self.gb_parser = genbank.GBparser()
def test_product_lists_mismatch(self):
diff --git a/tests/test_scheduler.py b/tests/test_scheduler.py
index 939de482..4bc3b047 100644
--- a/tests/test_scheduler.py
+++ b/tests/test_scheduler.py
@@ -3,27 +3,32 @@ Tests for the Scheduler module.
"""
-from utils import TEST_SETTINGS
-from mutalyzer.config import settings
-settings.configure(TEST_SETTINGS)
-
import os
import StringIO
#import logging; logging.basicConfig()
from nose.tools import *
+from mutalyzer.config import settings
from mutalyzer.db.models import BatchJob, BatchQueueItem
from mutalyzer import Db
from mutalyzer import File
from mutalyzer import output
from mutalyzer import Scheduler
+import utils
+
class TestScheduler():
"""
Test the Scheduler class.
"""
+ def setup(self):
+ utils.create_test_environment(database=True)
+
+ def teardown(self):
+ utils.destroy_environment()
+
@staticmethod
def _batch_job(variants, expected, job_type, argument=None):
file_instance = File.File(output.Output('test'))
@@ -32,7 +37,7 @@ class TestScheduler():
batch_file = StringIO.StringIO('\n'.join(variants) + '\n')
job, columns = file_instance.parseBatchFile(batch_file)
result_id = scheduler.addJob('test@test.test', job, columns,
- 'webservice', job_type, argument)
+ None, job_type, argument)
left = BatchQueueItem.query \
.join(BatchJob) \
@@ -72,8 +77,6 @@ class TestScheduler():
Simple name checker batch job.
"""
variants = ['AB026906.1:c.274G>T',
- 'NM_000059:c.670dup',
- 'NM_000059:c.670G>T',
'NM_000059.3:c.670G>T']
expected = [['AB026906.1:c.274G>T',
'(GenRecord): No mRNA field found for gene SDHD, '
@@ -95,7 +98,33 @@ class TestScheduler():
'AB026906.1(SDHD_i001):p.(Asp92Tyr)',
'CviQI,RsaI',
'BccI'],
- ['NM_000059:c.670dup',
+ ['NM_000059.3:c.670G>T',
+ '',
+ 'NM_000059.3',
+ 'BRCA2_v001',
+ 'c.670G>T',
+ 'n.897G>T',
+ 'c.670G>T',
+ 'p.(Asp224Tyr)',
+ 'BRCA2_v001:c.670G>T',
+ 'BRCA2_v001:p.(Asp224Tyr)',
+ '',
+ 'NM_000059.3',
+ 'NP_000050.2',
+ 'NM_000059.3(BRCA2_v001):c.670G>T',
+ 'NM_000059.3(BRCA2_i001):p.(Asp224Tyr)',
+ '',
+ 'BspHI,CviAII,FatI,Hpy188III,NlaIII']]
+ self._batch_job(variants, expected, 'NameChecker')
+
+ def test_name_checker_altered(self):
+ """
+ Name checker job with altered entries.
+ """
+ variants = ['NM_000059:c.670dup',
+ 'NM_000059:c.670G>T',
+ 'NM_000059.3:c.670G>T']
+ expected = [['NM_000059:c.670dup',
'|'.join(['(Retriever): No version number is given, '
'using NM_000059.3. Please use this number to '
'reduce downloading overhead.',
@@ -152,3 +181,35 @@ class TestScheduler():
'',
'BspHI,CviAII,FatI,Hpy188III,NlaIII']]
self._batch_job(variants, expected, 'NameChecker')
+
+ def test_name_checker_skipped(self):
+ """
+ Name checker job with skipped entries.
+ """
+ variants = ['NM_1234567890.3:c.670G>T',
+ 'NM_1234567890.3:c.570G>T',
+ 'NM_000059.3:c.670G>T']
+ expected = [['NM_1234567890.3:c.670G>T',
+ '(Retriever): Could not retrieve NM_1234567890.3.|'
+ '(Scheduler): All further occurrences with '
+ '\'NM_1234567890.3\' will be skipped'],
+ ['NM_1234567890.3:c.570G>T',
+ '(Scheduler): Skipping entry'],
+ ['NM_000059.3:c.670G>T',
+ '',
+ 'NM_000059.3',
+ 'BRCA2_v001',
+ 'c.670G>T',
+ 'n.897G>T',
+ 'c.670G>T',
+ 'p.(Asp224Tyr)',
+ 'BRCA2_v001:c.670G>T',
+ 'BRCA2_v001:p.(Asp224Tyr)',
+ '',
+ 'NM_000059.3',
+ 'NP_000050.2',
+ 'NM_000059.3(BRCA2_v001):c.670G>T',
+ 'NM_000059.3(BRCA2_i001):p.(Asp224Tyr)',
+ '',
+ 'BspHI,CviAII,FatI,Hpy188III,NlaIII']]
+ self._batch_job(variants, expected, 'NameChecker')
diff --git a/tests/test_services_json.py b/tests/test_services_json.py
index 35bbd180..122d9566 100644
--- a/tests/test_services_json.py
+++ b/tests/test_services_json.py
@@ -3,16 +3,14 @@ Tests for the JSON interface to Mutalyzer.
"""
-from utils import TEST_SETTINGS
-from mutalyzer.config import settings
-settings.configure(TEST_SETTINGS)
-
from nose.tools import *
import simplejson as json
from spyne.server.null import NullServer
import mutalyzer
from mutalyzer.services.json import application
+import utils
+
# Todo: We currently have no way of testing POST requests to the JSON API. We
# had some tests for this, but they were removed with the new setup [1].
@@ -26,10 +24,11 @@ class TestServicesJson():
"""
Test the Mutalyzer HTTP/RPC+JSON interface.
"""
- def setUp(self):
+ def setup(self):
"""
Initialize test server.
"""
+ utils.create_test_environment(database=True)
self.server = NullServer(application, ostr=True)
def _call(self, method, *args, **kwargs):
diff --git a/tests/test_services_soap.py b/tests/test_services_soap.py
index cea1ca25..46f3977c 100644
--- a/tests/test_services_soap.py
+++ b/tests/test_services_soap.py
@@ -3,10 +3,6 @@ Tests for the SOAP interface to Mutalyzer.
"""
-from utils import TEST_SETTINGS
-from mutalyzer.config import settings
-settings.configure(TEST_SETTINGS)
-
import datetime
import logging
import os
@@ -25,6 +21,7 @@ from mutalyzer.services.soap import application
from mutalyzer.sync import CacheSync
from mutalyzer.util import slow
+import utils
# Suds logs an awful lot of things with level=DEBUG, including entire WSDL
# files and SOAP responses. On any error, this is all dumped to the console,
@@ -52,10 +49,11 @@ class TestServicesSoap():
"""
Test the Mutalyzer SOAP interface.
"""
- def setUp(self):
+ def setup(self):
"""
Initialize test server.
"""
+ utils.create_test_environment(database=True)
self.server = NullServer(application, ostr=True)
# Unfortunately there's no easy way to just give a SUDS client a
# complete WSDL string, it only accepts a URL to it. So we create one.
diff --git a/tests/test_variantchecker.py b/tests/test_variantchecker.py
index 78033e3f..138550f0 100644
--- a/tests/test_variantchecker.py
+++ b/tests/test_variantchecker.py
@@ -3,10 +3,6 @@ Tests for the variantchecker module.
"""
-from utils import TEST_SETTINGS
-from mutalyzer.config import settings
-settings.configure(TEST_SETTINGS)
-
#import logging; logging.basicConfig()
from nose.tools import *
@@ -15,15 +11,18 @@ from mutalyzer.Db import Cache
from mutalyzer.Retriever import GenBankRetriever
from mutalyzer.variantchecker import check_variant
+import utils
+
class TestVariantchecker():
"""
Test the variantchecker module.
"""
- def setUp(self):
+ def setup(self):
"""
Initialize test variantchecker module.
"""
+ utils.create_test_environment(database=True)
self.output = Output(__file__)
self.cache_database = Cache()
self.retriever = GenBankRetriever(self.output, self.cache_database)
diff --git a/tests/test_website.py b/tests/test_website.py
index 02b1de9f..8607cac1 100644
--- a/tests/test_website.py
+++ b/tests/test_website.py
@@ -1,20 +1,10 @@
"""
Tests for the WSGI interface to Mutalyzer.
-Uses WebTest, see:
- http://pythonpaste.org/webtest/
- http://blog.ianbicking.org/2010/04/02/webtest-http-testing/
-
-I just installed webtest by 'easy_install webtest'.
-
@todo: Tests for /upload.
"""
-from utils import TEST_SETTINGS
-from mutalyzer.config import settings
-settings.configure(TEST_SETTINGS)
-
#import logging; logging.basicConfig()
import os
import re
@@ -27,18 +17,11 @@ import logging
import urllib
import cgi
-
import mutalyzer
from mutalyzer import website
from mutalyzer.util import slow, skip
-
-# TAL logs an awful lot of things with level=DEBUG. On any error, this is all
-# dumped to the console, which is very unconvenient. The following suppresses
-# most of this.
-logging.raiseExceptions = 0
-logging.basicConfig(level=logging.INFO)
-logging.getLogger('simpleTAL.HTMLTemplateCompiler').setLevel(logging.ERROR)
+import utils
BATCH_RESULT_URL = 'http://localhost/mutalyzer/Results_{id}.txt'
@@ -49,10 +32,11 @@ class TestWSGI():
Test the Mutalyzer WSGI interface.
"""
- def setUp(self):
+ def setup(self):
"""
Initialize test application.
"""
+ utils.create_test_environment(database=True)
web.config.debug = False
application = website.app.wsgifunc()
self.app = TestApp(application)
diff --git a/tests/utils.py b/tests/utils.py
index c119d67b..db1c39b6 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -1,14 +1,32 @@
import os
+import shutil
import tempfile
+from mutalyzer.config import settings
+from mutalyzer.db import models
-log_handle, log_filename = tempfile.mkstemp()
-os.close(log_handle)
+def create_test_environment(database=False):
+ """
+ Configure Mutalyzer for unit tests. All storage is transient and isolated.
+ """
+ log_handle, log_filename = tempfile.mkstemp()
+ os.close(log_handle)
-TEST_SETTINGS = dict(
- DEBUG = True,
- TESTING = True,
- CACHE_DIR = tempfile.mkdtemp(),
- LOG_FILE = log_filename
-)
+ settings.configure(dict(
+ DEBUG = True,
+ TESTING = True,
+ CACHE_DIR = tempfile.mkdtemp(),
+ DATABASE_URI = 'sqlite://',
+ LOG_FILE = log_filename))
+
+ if database:
+ models.create_all()
+
+
+def destroy_environment():
+ """
+ Destroy all storage defined in the current environment.
+ """
+ shutil.rmtree(settings.CACHE_DIR)
+ os.unlink(settings.LOG_FILE)
--
GitLab