From f2a6cc59b6b33675ef08cfdf0d9302ed7bcb2801 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Fri, 3 Jan 2014 21:48:39 +0100
Subject: [PATCH] Some fixes for running the unit tests
---
tests/test_crossmap.py | 3 +++
tests/test_describe.py | 3 +++
tests/test_grammar.py | 3 +++
tests/test_mapping.py | 5 ++--
tests/test_mutator.py | 3 +++
tests/test_parsers_genbank.py | 3 +++
tests/test_services_json.py | 3 +++
tests/test_services_soap.py | 6 ++---
tests/test_variantchecker.py | 12 ++++++----
tests/test_website.py | 43 +++++++++++++++++++++++------------
tests/utils.py | 3 +++
11 files changed, 63 insertions(+), 24 deletions(-)
diff --git a/tests/test_crossmap.py b/tests/test_crossmap.py
index 489e4252..2fdeffad 100644
--- a/tests/test_crossmap.py
+++ b/tests/test_crossmap.py
@@ -18,6 +18,9 @@ class TestCrossmap():
def setup(self):
utils.create_test_environment(database=True)
+ def teardown(self):
+ utils.destroy_environment()
+
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 9974709a..c922deed 100644
--- a/tests/test_describe.py
+++ b/tests/test_describe.py
@@ -20,6 +20,9 @@ class TestDescribe():
def setup(self):
utils.create_test_environment()
+ def teardown(self):
+ utils.destroy_environment()
+
def test1(self):
"""
Test 1.
diff --git a/tests/test_grammar.py b/tests/test_grammar.py
index 9abf02d8..3253ad77 100644
--- a/tests/test_grammar.py
+++ b/tests/test_grammar.py
@@ -26,6 +26,9 @@ class TestGrammar():
self.output = Output(__file__)
self.grammar = Grammar(self.output)
+ def teardown(self):
+ utils.destroy_environment()
+
def _parse(self, description):
"""
Parse a variant description.
diff --git a/tests/test_mapping.py b/tests/test_mapping.py
index 8c4e6c59..91b9ff8b 100644
--- a/tests/test_mapping.py
+++ b/tests/test_mapping.py
@@ -23,6 +23,9 @@ class TestConverter():
utils.create_test_environment(database=True)
self.output = Output(__file__)
+ def teardown(self):
+ utils.destroy_environment()
+
def _converter(self, build):
"""
Create a Converter instance for a given build.
@@ -111,8 +114,6 @@ class TestConverter():
assert 'NM_001007553.2:c.3863delA' not in coding
assert 'NM_001007553.1:c.*953delA' in coding
assert 'NM_001130523.1:c.*953delA' in coding
- assert 'NM_001007553.2:c.*953delA' in coding
- assert 'NM_001130523.2:c.*953delA' in coding
def test_S_Venkata_Suresh_Kumar_more(self):
"""
diff --git a/tests/test_mutator.py b/tests/test_mutator.py
index 6f8391ce..cc15f0e3 100644
--- a/tests/test_mutator.py
+++ b/tests/test_mutator.py
@@ -39,6 +39,9 @@ class TestMutator():
utils.create_test_environment()
self.output = Output(__file__)
+ def teardown(self):
+ utils.destroy_environment()
+
def _mutator(self, sequence):
"""
Create a Mutator instance for a given sequence.
diff --git a/tests/test_parsers_genbank.py b/tests/test_parsers_genbank.py
index a574cfb4..ec8083b0 100644
--- a/tests/test_parsers_genbank.py
+++ b/tests/test_parsers_genbank.py
@@ -22,6 +22,9 @@ class TestMutator():
utils.create_test_environment(database=True)
self.gb_parser = genbank.GBparser()
+ def teardown(self):
+ utils.destroy_environment()
+
def test_product_lists_mismatch(self):
"""
Test finding mismatches in some product lists.
diff --git a/tests/test_services_json.py b/tests/test_services_json.py
index 122d9566..9b2f4e80 100644
--- a/tests/test_services_json.py
+++ b/tests/test_services_json.py
@@ -31,6 +31,9 @@ class TestServicesJson():
utils.create_test_environment(database=True)
self.server = NullServer(application, ostr=True)
+ def teardown(self):
+ utils.destroy_environment()
+
def _call(self, method, *args, **kwargs):
r = getattr(self.server.service, method)(*args, **kwargs)
return json.loads(''.join(r))
diff --git a/tests/test_services_soap.py b/tests/test_services_soap.py
index 5225b7c1..ed5b3e6b 100644
--- a/tests/test_services_soap.py
+++ b/tests/test_services_soap.py
@@ -60,10 +60,11 @@ class TestServicesSoap():
self.wsdl = _write_wsdl(self.server)
self.client = Client('file://%s' % self.wsdl, cache=None)
- def tearDown(self):
+ def teardown(self):
"""
Remove temporary file used for WSDL.
"""
+ utils.destroy_environment()
os.unlink(self.wsdl)
def _call(self, method, *args, **kwargs):
@@ -332,9 +333,8 @@ class TestServicesSoap():
"""
created_since = datetime.datetime.today() - datetime.timedelta(days=14)
- database = Db.Cache()
output = Output(__file__)
- sync = CacheSync(output, database)
+ sync = CacheSync(output)
cache = sync.local_cache(created_since)
r = self._call('getCache', created_since)
diff --git a/tests/test_variantchecker.py b/tests/test_variantchecker.py
index e36de26a..a2ac64b8 100644
--- a/tests/test_variantchecker.py
+++ b/tests/test_variantchecker.py
@@ -7,7 +7,6 @@ Tests for the variantchecker module.
from nose.tools import *
from mutalyzer.output import Output
-from mutalyzer.Db import Cache
from mutalyzer.Retriever import GenBankRetriever
from mutalyzer.variantchecker import check_variant
from mutalyzer.util import slow, skip
@@ -25,8 +24,10 @@ class TestVariantchecker():
"""
utils.create_test_environment(database=True)
self.output = Output(__file__)
- self.cache_database = Cache()
- self.retriever = GenBankRetriever(self.output, self.cache_database)
+ self.retriever = GenBankRetriever(self.output)
+
+ def teardown(self):
+ utils.destroy_environment()
def _slice(self, chromosome, start, stop, orientation):
"""
@@ -846,7 +847,7 @@ class TestVariantchecker():
ud = self._slice_gene('A1BG') # Contains ZNF497 (v1 and v2) with no mRNA
check_variant(ud + '(A1BG_v001):c.13del', self.output)
wnomrna_other = self.output.getMessagesWithErrorCode('WNOMRNA_OTHER')
- assert len(wnomrna_other) == 2
+ assert len(wnomrna_other) == 3
def test_wnomrna(self):
"""
@@ -857,7 +858,8 @@ class TestVariantchecker():
check_variant(ud + '(ZNF497_v001):c.13del', self.output)
wnomrna = self.output.getMessagesWithErrorCode('WNOMRNA')
wnomrna_other = self.output.getMessagesWithErrorCode('WNOMRNA_OTHER')
- assert len(wnomrna) == len(wnomrna_other) == 1
+ assert len(wnomrna) == 1
+ assert len(wnomrna_other) == 2
def test_mrna_ref_adjacent_exons_warn(self):
"""
diff --git a/tests/test_website.py b/tests/test_website.py
index 56b06d07..1d3816fb 100644
--- a/tests/test_website.py
+++ b/tests/test_website.py
@@ -17,6 +17,19 @@ import logging
import urllib
import cgi
+# Todo: Since the `mutalyzer.website` module accesses the configuration
+# settings at import time, we need to pre-populate those. This hack can
+# be removed once we moved from web.py to Flask and refactored the web
+# application into an application factory (which does not access the
+# configuration settings at import time).
+from mutalyzer.config import settings
+settings.configure(dict(
+ DEBUG = True,
+ TESTING = True,
+ CACHE_DIR = None,
+ DATABASE_URI = 'sqlite://',
+ LOG_FILE = None))
+
import mutalyzer
from mutalyzer import website
from mutalyzer.util import slow, skip
@@ -31,7 +44,6 @@ class TestWSGI():
"""
Test the Mutalyzer WSGI interface.
"""
-
def setup(self):
"""
Initialize test application.
@@ -41,6 +53,9 @@ class TestWSGI():
application = website.app.wsgifunc()
self.app = TestApp(application)
+ def teardown(self):
+ utils.destroy_environment()
+
def test_root(self):
"""
Expect the index HTML page.
@@ -52,7 +67,7 @@ class TestWSGI():
assert_equal(r.status, '200 OK')
# We check for <html> to make sure the menu template is included
r.mustcontain('<html>',
- 'Welcome to the Mutalyzer web site',
+ 'Welcome to the Mutalyzer website',
'</html>')
def test_index(self):
@@ -63,7 +78,7 @@ class TestWSGI():
assert_equal(r.status, '200 OK')
# We check for <html> to make sure the menu template is included
r.mustcontain('<html>',
- 'Welcome to the Mutalyzer web site',
+ 'Welcome to the Mutalyzer website',
'</html>')
def test_index_explicit(self):
@@ -74,7 +89,7 @@ class TestWSGI():
assert_equal(r.status, '200 OK')
# We check for <html> to make sure the menu template is included
r.mustcontain('<html>',
- 'Welcome to the Mutalyzer web site',
+ 'Welcome to the Mutalyzer website',
'</html>')
def test_about(self):
@@ -151,7 +166,7 @@ class TestWSGI():
'0 Warnings',
'Raw variant 1: deletion of 1',
'<a href="#bottom" class="hornav">go to bottom</a>',
- '<input value="NM_002001.2:g.1del" type="text" name="name" style="width:100%">')
+ '<input type="text" name="name" value="NM_002001.2:g.1del" style="width:100%">')
def test_check_more_valid(self):
"""
@@ -225,7 +240,7 @@ class TestWSGI():
"""
r = self.app.get('/check?name=NM_002001.2:g.1del&standalone=1')
assert_false('<a href="#bottom" class="hornav">go to bottom</a>' in r)
- assert_false('<input value="NM_002001.2:g.1del" type="text" name="name" style="width:100%">' in r)
+ assert_false('<input type="text" name="name" value="NM_002001.2:g.1del" style="width:100%">' in r)
r.mustcontain('0 Errors',
'0 Warnings',
'Raw variant 1: deletion of 1',
@@ -296,7 +311,7 @@ class TestWSGI():
'0 Warnings',
'Raw variant 1: deletion of 1',
'<a href="#bottom" class="hornav">go to bottom</a>',
- '<input value="NM_002001.2:g.1del" type="text" name="name" style="width:100%">')
+ '<input type="text" name="name" value="NM_002001.2:g.1del" style="width:100%">')
def test_snp_converter_valid(self):
"""
@@ -308,9 +323,9 @@ class TestWSGI():
r = form.submit()
r.mustcontain('0 Errors',
'0 Warnings',
- 'NC_000011.9:g.111959625C>T',
- 'NG_012337.2:g.7055C>T',
- 'NM_003002.3:c.204C>T',
+ 'NC_000011.9:g.111959625C>T',
+ 'NG_012337.2:g.7055C>T',
+ 'NM_003002.3:c.204C>T',
'NP_002993.1:p.Ser68=')
def test_snp_converter_invalid(self):
@@ -335,7 +350,7 @@ class TestWSGI():
form['build'] = 'hg19'
form['variant'] = 'NM_003002.2:c.204C>T'
r = form.submit()
- r.mustcontain('NC_000011.9:g.111959625C>T')
+ r.mustcontain('NC_000011.9:g.111959625C>T')
def test_position_converter_g2c(self):
"""
@@ -346,7 +361,7 @@ class TestWSGI():
form['build'] = 'hg19'
form['variant'] = 'NC_000011.9:g.111959625C>T'
r = form.submit()
- r.mustcontain('NM_003002.2:c.204C>T')
+ r.mustcontain('NM_003002.2:c.204C>T')
@slow
def _batch(self, batch_type='NameChecker', arg1=None, file="", size=0,
@@ -780,7 +795,7 @@ facilisi."""
'1 Warning',
'Raw variant 1: substitution at 7872',
'<a href="#bottom" class="hornav">go to bottom</a>',
- '<input value="AB026906.1:c.274G>T" type="text" name="name" style="width:100%">')
+ '<input type="text" name="name" value="AB026906.1:c.274G>T" style="width:100%">')
r = self.app.get('/Reference/AB026906.1.gb')
assert_equal(r.content_type, 'text/plain')
assert_equal(r.content_length, 26427)
@@ -801,7 +816,7 @@ facilisi."""
'1 Warning',
'Raw variant 1: substitution at 7872',
'<a href="#bottom" class="hornav">go to bottom</a>',
- '<input value="AB026906.1:c.274G>T" type="text" name="name" style="width:100%">')
+ '<input type="text" name="name" value="AB026906.1:c.274G>T" style="width:100%">')
r = self.app.head('/Reference/AB026906.1.gb')
assert_equal(r.content_type, 'text/plain')
diff --git a/tests/utils.py b/tests/utils.py
index db1c39b6..aefac256 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -6,6 +6,9 @@ from mutalyzer.config import settings
from mutalyzer.db import models
+# Todo: Refactor creating and destroying environment into a context manager.
+
+
def create_test_environment(database=False):
"""
Configure Mutalyzer for unit tests. All storage is transient and isolated.
--
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