Updated unit tests. Now using the nose Python testing framework.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@224 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

INSTALL

@@ -15,6 +15,7 @@ This program depends on the following packages:
 - python-webpy     >= 0.33
 - python-webtest   >= 1.2.3
 - python-suds      >= 0.3.9-1
+- python-nose      >= 0.11
 
 The web and SOAP interfaces depend on the following packages:
 - apache2               >= 2.2.11

README

@@ -28,6 +28,8 @@ Todo:
   http://standards.freedesktop.org/basedir-spec/basedir-spec-latest.html
 * Document integration, deployment, release management, etc.
 * Use standard logging module, with rotating functionality.
+* Use environment variable for testing situation. Something like:
+  http://webpy.org/cookbook/testing_with_paste_and_nose
 
 
 Notes for server setup (Europium VM copy):

mutalyzer/tests/test_grammar.py

-#!/usr/bin/env python
-
 """
 Tests for the mutalyzer.grammar module.
 """
 
 #import logging; logging.basicConfig()
 import os
-import unittest
 import site
+from nose.tools import *
 
 # Todo: Can this be done in a more elegant way?
 os.chdir('../..')
@@ -18,7 +16,7 @@ from mutalyzer.grammar import Grammar
 from mutalyzer.output import Output
 
 
-class TestGrammar(unittest.TestCase):
+class TestGrammar():
     """
     Test the mytalyzer.grammar module.
     """
@@ -33,7 +31,7 @@ class TestGrammar(unittest.TestCase):
 
     def test_some_variants(self):
         """
-        No change, no shifts.
+        Some example variants.
         """
         self.grammar.parse('NM_002001.2:c.[12del]')
         self.grammar.parse('NM_002001.2:c.[(12del)]')
@@ -41,11 +39,3 @@ class TestGrammar(unittest.TestCase):
         self.grammar.parse('NM_002001.2:c.[(12del);(12del)]')
         self.grammar.parse('NM_002001.2:c.[(12del;12del)]')
         self.grammar.parse('NM_002001.2:c.[((12del)?;12del)?]')
-
-
-if __name__ == '__main__':
-    # Usage:
-    #   ./test_parser.py -v
-    # Or, selecting a specific test:
-    #   ./test_parser.py -v TestParser.test_some_variants
-    unittest.main()

mutalyzer/tests/test_mutalyzer.py

-#!/usr/bin/env python
-
 """
 Tests for the Mutalyzer module.
 """
@@ -8,8 +6,8 @@ Tests for the Mutalyzer module.
 import re
 import os
 import random
-import unittest
 import site
+from nose.tools import *
 from Bio.Seq import Seq
 
 # Todo: Can this be done in a more elegant way?
@@ -21,7 +19,7 @@ from mutalyzer.output import Output
 from mutalyzer.variantchecker import check_variant
 
 
-class TestMutalyzer(unittest.TestCase):
+class TestMutalyzer():
     """
     Test the Mutalyzer module.
     """
@@ -39,7 +37,7 @@ class TestMutalyzer(unittest.TestCase):
         """
         check_variant('NM_003002.2:c.273del', self.config, self.output)
         wroll = self.output.getMessagesWithErrorCode('WROLL')
-        self.assertTrue(len(wroll) > 0)
+        assert len(wroll) > 0
 
     def test_no_roll(self):
         """
@@ -47,7 +45,7 @@ class TestMutalyzer(unittest.TestCase):
         """
         check_variant('NM_003002.2:c.274del', self.config, self.output)
         wroll = self.output.getMessagesWithErrorCode('WROLL')
-        self.assertTrue(len(wroll) == 0)
+        assert len(wroll) == 0
 
     def test_no_roll_splice(self):
         """
@@ -55,9 +53,9 @@ class TestMutalyzer(unittest.TestCase):
         """
         check_variant('NM_000088.3:g.459del', self.config, self.output)
         wrollback = self.output.getMessagesWithErrorCode('IROLLBACK')
-        self.assertTrue(len(wrollback) > 0)
+        assert len(wrollback) > 0
         wroll = self.output.getMessagesWithErrorCode('WROLL')
-        self.assertTrue(len(wroll) == 0)
+        assert len(wroll) == 0
 
     def test_partial_roll_splice(self):
         """
@@ -66,9 +64,9 @@ class TestMutalyzer(unittest.TestCase):
         """
         check_variant('NM_000088.3:g.494del', self.config, self.output)
         wrollback = self.output.getMessagesWithErrorCode('IROLLBACK')
-        self.assertTrue(len(wrollback) > 0)
+        assert len(wrollback) > 0
         wroll = self.output.getMessagesWithErrorCode('WROLL')
-        self.assertTrue(len(wroll) > 0)
+        assert len(wroll) > 0
 
     def test_roll_after_splice(self):
         """
@@ -76,26 +74,18 @@ class TestMutalyzer(unittest.TestCase):
         """
         check_variant('NM_000088.3:g.460del', self.config, self.output)
         wroll = self.output.getMessagesWithErrorCode('WROLL')
-        self.assertTrue(len(wroll) > 0)
+        assert len(wroll) > 0
 
     def test_ins_cds_start(self):
         """
         Insertion on CDS start boundary should not be included in CDS.
         """
         check_variant('NM_000143.3:c.-1_1insCAT', self.config, self.output)
-        self.assertEqual(self.output.getIndexedOutput("newprotein", 0), None)
+        assert_equal(self.output.getIndexedOutput("newprotein", 0), None)
 
     def test_ins_cds_start_after(self):
         """
         Insertion after CDS start boundary should be included in CDS.
         """
         check_variant('NM_000143.3:c.1_2insCAT', self.config, self.output)
-        self.assertEqual(self.output.getIndexedOutput("newprotein", 0), '?')
-
-
-if __name__ == '__main__':
-    # Usage:
-    #   ./test_mutalyzer.py -v
-    # Or, selecting a specific test:
-    #   ./test_mutalyzer.py -v TestMutalyzer.test_ins_cds_start
-    unittest.main()
+        assert_equal(self.output.getIndexedOutput("newprotein", 0), '?')

mutalyzer/tests/test_webservice.py

-#!/usr/bin/env python
-
 """
 Tests for the SOAP interface to Mutalyzer.
 """
 
+
 import logging; logging.raiseExceptions = 0
 import urllib2
 from suds.client import Client
 from suds import WebFault
-import unittest
+from nose.tools import *
+
 
 WSDL_URL = 'http://mutalyzer.martijn/services/?wsdl'
 
-class TestWSDL(unittest.TestCase):
+
+class TestWSDL():
     """
     Test the Mutalyzer SOAP interface WSDL description.
     """
@@ -21,10 +22,11 @@ class TestWSDL(unittest.TestCase):
         Test if the WSDL is available and looks somewhat sensible.
         """
         wsdl = urllib2.urlopen(WSDL_URL).read()
-        self.assertTrue(wsdl.startswith("<?xml version='1.0' encoding='UTF-8'?>"))
-        self.assertTrue('name="Mutalyzer"' in wsdl)
+        assert wsdl.startswith("<?xml version='1.0' encoding='UTF-8'?>")
+        assert 'name="Mutalyzer"' in wsdl
+
 
-class TestWebservice(unittest.TestCase):
+class TestWebservice():
     """
     Test the Mutalyzer SOAP interface.
     """
@@ -43,7 +45,7 @@ class TestWebservice(unittest.TestCase):
         Running checkSyntax with a valid variant name should return True.
         """
         r = self.client.service.checkSyntax('AB026906.1:c.274G>T')
-        self.assertEqual(r.valid, True)
+        assert_equal(r.valid, True)
 
     def test_checksyntax_invalid(self):
         """
@@ -51,19 +53,15 @@ class TestWebservice(unittest.TestCase):
         and give at least one error message.
         """
         r = self.client.service.checkSyntax('0:abcd')
-        self.assertEqual(r.valid, False)
-        self.assertTrue(len(r.messages.SoapMessage) >= 1)
+        assert_equal(r.valid, False)
+        assert len(r.messages.SoapMessage) >= 1
 
+    @raises(WebFault)
     def test_checksyntax_empty(self):
         """
         Running checkSyntax with no variant name should raise exception.
         """
-        try:
-            self.client.service.checkSyntax()
-            self.fail('Expected WebFault exception')
-        except WebFault, e:
-            self.assertEqual(e.fault.faultstring,
-                             'The variant argument is not provided.')
+        self.client.service.checkSyntax()
 
     def test_transcriptinfo_valid(self):
         """
@@ -72,9 +70,9 @@ class TestWebservice(unittest.TestCase):
         """
         r = self.client.service.transcriptInfo(LOVD_ver='123', build='hg19',
                                                accNo='NM_002001.2')
-        self.assertEqual(r.trans_start, -99)
-        self.assertEqual(r.trans_stop, 1066)
-        self.assertEqual(r.CDS_stop, 774)
+        assert_equal(r.trans_start, -99)
+        assert_equal(r.trans_stop, 1066)
+        assert_equal(r.CDS_stop, 774)
 
     def test_numberconversion_gtoc_valid(self):
         """
@@ -83,8 +81,8 @@ class TestWebservice(unittest.TestCase):
         """
         r = self.client.service.numberConversion(build='hg19',
                                                  variant='NC_000001.10:g.159272155del')
-        self.assertEqual(type(r.string), list)
-        self.assertTrue('NM_002001.2:c.1del' in r.string)
+        assert_equal(type(r.string), list)
+        assert 'NM_002001.2:c.1del' in r.string
 
     def test_numberconversion_ctog_valid(self):
         """
@@ -93,8 +91,8 @@ class TestWebservice(unittest.TestCase):
         """
         r = self.client.service.numberConversion(build='hg19',
                                                  variant='NM_002001.2:c.1del')
-        self.assertEqual(type(r.string), list)
-        self.assertTrue('NC_000001.10:g.159272155del' in r.string)
+        assert_equal(type(r.string), list)
+        assert 'NC_000001.10:g.159272155del' in r.string
 
     def test_gettranscriptsbygenename_valid(self):
         """
@@ -103,7 +101,7 @@ class TestWebservice(unittest.TestCase):
         """
         r = self.client.service.getTranscriptsByGeneName(build='hg19',
                                                          name='DMD')
-        self.assertEqual(type(r.string), list)
+        assert_equal(type(r.string), list)
         for t in ['NM_004006.2',
                   'NM_000109.3',
                   'NM_004021.2',
@@ -111,7 +109,7 @@ class TestWebservice(unittest.TestCase):
                   'NM_004007.2',
                   'NM_004018.2',
                   'NM_004022.2']:
-            self.assertTrue(t in r.string)
+            assert t in r.string
 
     def test_gettranscriptsandinfo_valid(self):
         """
@@ -119,7 +117,7 @@ class TestWebservice(unittest.TestCase):
         give a list of TranscriptInfo objects.
         """
         r = self.client.service.getTranscriptsAndInfo('AL449423.14')
-        self.assertEqual(type(r.TranscriptInfo), list)
+        assert_equal(type(r.TranscriptInfo), list)
         names = [t.name for t in r.TranscriptInfo]
         for t in ['CDKN2B_v002',
                   'CDKN2B_v001',
@@ -128,7 +126,7 @@ class TestWebservice(unittest.TestCase):
                   'CDKN2A_v007',
                   'C9orf53_v001',
                   'CDKN2A_v001']:
-            self.assertTrue(t in names)
+            assert t in names
 
     def test_gettranscriptsandinfo_restricted_valid(self):
         """
@@ -137,20 +135,13 @@ class TestWebservice(unittest.TestCase):
         to the gene.
         """
         r = self.client.service.getTranscriptsAndInfo('AL449423.14', 'CDKN2A')
-        self.assertEqual(type(r.TranscriptInfo), list)
+        assert_equal(type(r.TranscriptInfo), list)
         names = [t.name for t in r.TranscriptInfo]
         for t in ['CDKN2A_v008',
                   'CDKN2A_v007']:
-            self.assertTrue(t in names)
+            assert t in names
         for t in ['CDKN2B_v002',
                   'CDKN2B_v001',
                   'MTAP_v005',
                   'C9orf53_v001']:
-            self.assertFalse(t in names)
-
-if __name__ == '__main__':
-    # Usage:
-    #   ./test_webservice.py -v
-    # Or, selecting a specific test:
-    #   ./test_webservice.py -v TestWebservice.test_checksyntax_empty
-    unittest.main()
+            assert_false(t in names)

mutalyzer/tests/test_wsgi.py

-#!/usr/bin/env python
-
 """
 Tests for the WSGI interface to Mutalyzer.
 
@@ -12,10 +10,11 @@ I just installed webtest by 'easy_install webtest'.
 @todo: Tests for /upload.
 """
 
+
 #import logging; logging.basicConfig()
 import re
 import time
-import unittest
+from nose.tools import *
 from webtest import TestApp
 
 # Todo: Can this be done in a more elegant way?
@@ -23,7 +22,8 @@ import site
 site.addsitedir('../..')
 from mutalyzer.wsgi import application
 
-class TestWSGI(unittest.TestCase):
+
+class TestWSGI():
     """
     Test the Mutalyzer WSGI interface.
     """
@@ -39,7 +39,7 @@ class TestWSGI(unittest.TestCase):
         Expect the index HTML page.
         """
         r = self.app.get('/')
-        self.assertEqual(r.status, '200 OK')
+        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',
@@ -131,8 +131,8 @@ class TestWSGI(unittest.TestCase):
         Should not include form and main layout HTML.
         """
         r = self.app.get('/check?mutationName=NM_002001.2:g.1del')
-        self.assertFalse('<a href="#bottom" class="hornav">go to bottom</a>' in r)
-        self.assertFalse('<input value="NM_002001.2:g.1del" type="text" name="mutationName" style="width:100%">' in r)
+        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="mutationName" style="width:100%">' in r)
         r.mustcontain('0 Errors',
                       '0 Warnings',
                       'Raw variant 1: deletion of 1',
@@ -145,8 +145,8 @@ class TestWSGI(unittest.TestCase):
         redirect to the name checker.
         """
         r = self.app.get('/checkForward?mutationName=NM_002001.2:g.1del')
-        self.assertEqual(r.status, '303 See Other')
-        self.assertTrue(r.location.endswith('/check'))
+        assert_equal(r.status, '303 See Other')
+        assert r.location.endswith('/check')
         r = r.follow()
         r.mustcontain('0 Errors',
                       '0 Warnings',
@@ -229,16 +229,16 @@ class TestWSGI(unittest.TestCase):
         max_tries = 60
         for i in range(max_tries):
             r = self.app.get('/progress?jobID=' + id + '&totalJobs=' + str(size) + '&ajax=1')
-            self.assertEqual(r.content_type, 'text/plain')
+            assert_equal(r.content_type, 'text/plain')
             #print '%s: %s' % (batch_type, r.body)
             if r.body == 'OK': break
-            self.assertTrue(re.match('[0-9]+', r.body))
+            assert re.match('[0-9]+', r.body)
             time.sleep(2)
-        self.assertEqual(r.body, 'OK')
+        assert_equal(r.body, 'OK')
         r = self.app.get('/Results_' + id + '.txt')
-        self.assertEqual(r.content_type, 'text/plain')
+        assert_equal(r.content_type, 'text/plain')
         r.mustcontain(header)
-        self.assertTrue(len(r.body.strip().split('\n')) == size + 1)
+        assert len(r.body.strip().split('\n')) == size + 1
 
     def test_batch_namechecker(self):
         """
@@ -401,14 +401,14 @@ facilisi."""
         form.set('batchFile', ('test_batch_toobig.txt',
                                file))
         r = form.submit(status=413)
-        self.assertEqual(r.content_type, 'text/plain')
+        assert_equal(r.content_type, 'text/plain')
 
     def test_download_py(self):
         """
         Download a Python example client for the webservice.
         """
         r = self.app.get('/download/client-suds.py')
-        self.assertEqual(r.content_type, 'text/plain')
+        assert_equal(r.content_type, 'text/plain')
         r.mustcontain('#!/usr/bin/env python')
 
     def test_download_rb(self):
@@ -416,7 +416,7 @@ facilisi."""
         Download a Ruby example client for the webservice.
         """
         r = self.app.get('/download/client-savon.rb')
-        self.assertEqual(r.content_type, 'text/plain')
+        assert_equal(r.content_type, 'text/plain')
         r.mustcontain('#!/usr/bin/env ruby')
 
     def test_download_cs(self):
@@ -424,7 +424,7 @@ facilisi."""
         Download a C# example client for the webservice.
         """
         r = self.app.get('/download/client-mono.cs')
-        self.assertEqual(r.content_type, 'text/plain')
+        assert_equal(r.content_type, 'text/plain')
         r.mustcontain('public static void Main(String [] args) {')
 
     def test_download_php(self):
@@ -432,7 +432,7 @@ facilisi."""
         Download a PHP example client for the webservice.
         """
         r = self.app.get('/download/client-php.php')
-        self.assertEqual(r.content_type, 'text/plain')
+        assert_equal(r.content_type, 'text/plain')
         r.mustcontain('<?php')
 
     def test_downloads_batchtest(self):
@@ -440,7 +440,7 @@ facilisi."""
         Download the batch test example file.
         """
         r = self.app.get('/downloads/batchtestnew.txt')
-        self.assertEqual(r.content_type, 'text/plain')
+        assert_equal(r.content_type, 'text/plain')
         r.mustcontain('NM_003002.1:c.3_4insG')
 
     def test_reference(self):
@@ -448,8 +448,8 @@ facilisi."""
         Download a reference file.
         """
         r = self.app.get('/Reference/AB026906.1.gb')
-        self.assertEqual(r.content_type, 'text/plain')
-        self.assertEqual(r.content_length, 26427)
+        assert_equal(r.content_type, 'text/plain')
+        assert_equal(r.content_length, 26427)
         r.mustcontain('ggaaaaagtc tctcaaaaaa cctgctttat')
 
     def test_soap_documentation(self):
@@ -457,7 +457,7 @@ facilisi."""
         Test the SOAP documentation generated from the WSDL.
         """
         r = self.app.get('/documentation')
-        self.assertEqual(r.content_type, 'text/html')
+        assert_equal(r.content_type, 'text/html')
         r.mustcontain('Web Service: Mutalyzer')
 
     def test_getgs(self):
@@ -468,26 +468,26 @@ facilisi."""
         r.mustcontain('0 Errors',
                       '0 Warnings',
                       'Raw variant 1: substitution at 7055')
-        self.assertTrue(r.body.find('go to bottom') == -1)
-        self.assertTrue(r.body.find('<input') == -1)
+        assert r.body.find('go to bottom') == -1
+        assert r.body.find('<input') == -1
 
     def test_variantinfo_g2c(self):
         """
         Test the /Variant_info interface used by LOVD2 (g to c).
         """
         r = self.app.get('/Variant_info?LOVD_ver=2.0-29&build=hg19&acc=NM_203473.1&var=g.48374289_48374389del')
-        self.assertEqual(r.content_type, 'text/plain')
+        assert_equal(r.content_type, 'text/plain')
         expected = '\n'.join(['1020', '0', '1072', '48', '48374289', '48374389', 'del'])
-        self.assertEqual(r.body, expected)
+        assert_equal(r.body, expected)
 
     def test_variantinfo_c2g(self):
         """
         Test the /Variant_info interface used by LOVD2 (c to g).
         """
         r = self.app.get('/Variant_info?LOVD_ver=2.0-29&build=hg19&acc=NM_203473.1&var=c.1020_1072%2B48del')
-        self.assertEqual(r.content_type, 'text/plain')
+        assert_equal(r.content_type, 'text/plain')
         expected = '\n'.join(['1020', '0', '1072', '48', '48374289', '48374389', 'del'])
-        self.assertEqual(r.body, expected)
+        assert_equal(r.body, expected)
 
     def test_variantinfo_c2g_downstream(self):
         """
@@ -495,9 +495,9 @@ facilisi."""
         notation to g).
         """
         r = self.app.get('/Variant_info?LOVD_ver=2.0-29&build=hg19&acc=NM_203473.1&var=c.1709%2Bd187del')
-        self.assertEqual(r.content_type, 'text/plain')
+        assert_equal(r.content_type, 'text/plain')
         expected = '\n'.join(['1709', '187', '1709', '187', '48379389', '48379389', 'del'])
-        self.assertEqual(r.body, expected)
+        assert_equal(r.body, expected)
 
     def test_upload_local_file(self):
         """
@@ -513,10 +513,3 @@ facilisi."""
                                   open(test_genbank_file, 'r').read()))
         r = form.submit()
         r.mustcontain('Your reference sequence was uploaded successfully.')
-
-if __name__ == '__main__':
-    # Usage:
-    #   ./test_wsgi.py -v
-    # Or, selecting a specific test:
-    #   ./test_wsgi.py -v TestWSGI.test_getgs
-    unittest.main()

mutalyzer/util.py

@@ -351,9 +351,9 @@ def trim_common(s1, s2):
     """
     Given two strings, trim their longest common prefix and suffix.
 
-        >>> util.trim_common('abcdefg', 'abcabcdefg')
+        >>> trim_common('abcdefg', 'abcabcdefg')
         ('', 'abc', 3, 4)
-        >>> util.trim_common('abcxyzefg', 'abcabcg')
+        >>> trim_common('abcxyzefg', 'abcabcg')
         ('xyzef', 'abc', 3, 1)
 
     @arg s1: A string.