From 4190406e61010f947afb10f578980b76e27a4881 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Tue, 10 Jul 2012 17:29:00 -0700 Subject: [PATCH] Test reading the xml out of a file too. You write some code and think "oh this is simple, it should be ok without tests" and then you watch the stack traces. Now its tested -- at least a bit. --- htsworkflow/pipelines/test/test_genomemap.py | 27 ++++++++++++++++---- 1 file changed, 22 insertions(+), 5 deletions(-) diff --git a/htsworkflow/pipelines/test/test_genomemap.py b/htsworkflow/pipelines/test/test_genomemap.py index 421308d..d0c1e66 100644 --- a/htsworkflow/pipelines/test/test_genomemap.py +++ b/htsworkflow/pipelines/test/test_genomemap.py @@ -10,19 +10,36 @@ import unittest from htsworkflow.pipelines.runfolder import ElementTree from htsworkflow.pipelines import genomemap -class TestGenomeMap(unittest.TestCase): - def test_genomesizes_xml(self): - xml = ElementTree.fromstring(""" +MINI_GENOME_XML = ''' - -""") + +''' +class TestGenomeMap(unittest.TestCase): + def test_genomesizes_xml(self): + xml = ElementTree.fromstring(MINI_GENOME_XML) g = genomemap.GenomeMap() g.build_map_from_element(xml) self.assertTrue('chr1.fa' in g) self.assertEqual(g['chr1.fa'], 'mm9/chr1.fa') + def test_genomesizes_file(self): + g = genomemap.GenomeMap() + try: + tempdir = tempfile.mkdtemp(prefix='tmp_genome') + name = os.path.join(tempdir, '11111_NoIndex_L001_genomesize.xml') + stream = open(name, 'w') + stream.write(MINI_GENOME_XML) + stream.close() + g.parse_genomesize(name) + finally: + shutil.rmtree(tempdir) + + self.assertTrue('chr1.fa' in g) + self.assertEqual(len(g), 2) + self.assertEqual(g['chr1.fa'], 'mm9/chr1.fa') + def test_simulated_genome_dir(self): vlds = [genomemap.vldInfo('chr1.fa.vld', False), genomemap.vldInfo('chr2.fa.vld', False), -- 2.30.2