From 187f5cc127a79f6a547511bb7a894b5080180fb9 Mon Sep 17 00:00:00 2001 From: Andreas Tille Date: Tue, 21 Jul 2015 11:48:54 +0200 Subject: [PATCH] Remove tests relying on online connection from test suite --- debian/changelog | 8 ++- debian/patches/series | 1 + debian/patches/strip_online_tests.patch | 82 +++++++++++++++++++++++++ 3 files changed, 89 insertions(+), 2 deletions(-) create mode 100644 debian/patches/strip_online_tests.patch diff --git a/debian/changelog b/debian/changelog index 8c9cb7a..819e0cd 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,12 +1,16 @@ -python-pysam (0.8.3+ds1-2) UNRELEASED; urgency=medium +python-pysam (0.8.3+ds1-3) UNRELEASED; urgency=medium + [ Afif Elghraoui ] * Team upload. * Improve python3 compatibility for upstream test sources * Refresh older patches * Fix autopkgtests * Do not provide test data package - -- Afif Elghraoui Sat, 11 Jul 2015 01:02:16 -0700 + [ Andreas Tille ] + * Remove tests relying on online connection from test suite + + -- Andreas Tille Tue, 21 Jul 2015 11:48:37 +0200 python-pysam (0.8.3+ds1-1) experimental; urgency=medium diff --git a/debian/patches/series b/debian/patches/series index 951529b..55ab446 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -4,3 +4,4 @@ correct-spelling-errors.patch ignore-htslib-dir.patch improve-python3-compatibility.patch sam_mpileup.patch +strip_online_tests.patch diff --git a/debian/patches/strip_online_tests.patch b/debian/patches/strip_online_tests.patch new file mode 100644 index 0000000..c2bc21f --- /dev/null +++ b/debian/patches/strip_online_tests.patch @@ -0,0 +1,82 @@ +Author: Andreas Tille +Last-Update: Tue, 21 Jul 2015 11:39:00 +0200 +Description: Remove tests relying on online connection from test suite + +--- a/tests/AlignmentFile_test.py ++++ b/tests/AlignmentFile_test.py +@@ -1730,49 +1730,6 @@ class TestRemoteFileFTP(unittest.TestCas + self.assertEqual(len(result), 36) + + +-class TestRemoteFileHTTP(unittest.TestCase): +- +- url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/ex1.bam" +- region = "chr1:1-1000" +- local = os.path.join(DATADIR, "ex1.bam") +- +- def testView(self): +- if not checkURL(self.url): +- return +- +- samfile_local = pysam.AlignmentFile(self.local, "rb") +- ref = list(samfile_local.fetch(region=self.region)) +- +- result = pysam.view(self.url, self.region) +- self.assertEqual(len(result), len(ref)) +- +- def testFetch(self): +- if not checkURL(self.url): +- return +- +- samfile = pysam.AlignmentFile(self.url, "rb") +- result = list(samfile.fetch(region=self.region)) +- samfile_local = pysam.AlignmentFile(self.local, "rb") +- ref = list(samfile_local.fetch(region=self.region)) +- +- self.assertEqual(len(ref), len(result)) +- for x, y in zip(result, ref): +- self.assertEqual(x.compare(y), 0) +- +- def testFetchAll(self): +- if not checkURL(self.url): +- return +- +- samfile = pysam.AlignmentFile(self.url, "rb") +- result = list(samfile.fetch()) +- samfile_local = pysam.AlignmentFile(self.local, "rb") +- ref = list(samfile_local.fetch()) +- +- self.assertEqual(len(ref), len(result)) +- for x, y in zip(result, ref): +- self.assertEqual(x.compare(y), 0) +- +- + class TestLargeOptValues(unittest.TestCase): + + ints = (65536, 214748, 2147484, 2147483647) +--- a/tests/tabix_test.py ++++ b/tests/tabix_test.py +@@ -927,23 +927,6 @@ for vcf_file in vcf_files: + ############################################################################ + + +-class TestRemoteFileHTTP(unittest.TestCase): +- +- url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_htslib.gtf.gz" +- region = "chr1:1-1000" +- local = os.path.join(DATADIR, "example.gtf.gz") +- +- def testFetchAll(self): +- remote_file = pysam.TabixFile(self.url, "r") +- remote_result = list(remote_file.fetch()) +- local_file = pysam.TabixFile(self.local, "r") +- local_result = list(local_file.fetch()) +- +- self.assertEqual(len(remote_result), len(local_result)) +- for x, y in zip(remote_result, local_result): +- self.assertEqual(x, y) +- +- + class TestIndexArgument(unittest.TestCase): + + filename_src = os.path.join(DATADIR, "example.vcf.gz") -- 2.30.2