From eeec80eca5a393156ce1b323f53c3576c4d99f6a Mon Sep 17 00:00:00 2001
From: Afif Elghraoui <afif@ghraoui.name>
Date: Fri, 13 Nov 2015 20:48:49 -0800
Subject: [PATCH] Replace patch for network-dependent tests

---
 .../disable-tests-requiring-network.patch     | 42 ++++++++++
 debian/patches/series                         |  2 +-
 debian/patches/strip_online_tests.patch       | 82 -------------------
 3 files changed, 43 insertions(+), 83 deletions(-)
 create mode 100644 debian/patches/disable-tests-requiring-network.patch
 delete mode 100644 debian/patches/strip_online_tests.patch

diff --git a/debian/patches/disable-tests-requiring-network.patch b/debian/patches/disable-tests-requiring-network.patch
new file mode 100644
index 0000000..07af1b6
--- /dev/null
+++ b/debian/patches/disable-tests-requiring-network.patch
@@ -0,0 +1,42 @@
+Description: Disable tests requiring network access
+Author: Afif Elghraoui <afif@ghraoui.name>
+Forwarded: no
+Last-Update: 2015-11-13
+--- python-pysam.orig/tests/tabix_test.py
++++ python-pysam/tests/tabix_test.py
+@@ -504,7 +504,7 @@
+         b = copy.copy(a)
+         self.assertEqual(a, b)
+ 
+-        
++
+ 
+ class TestIterators(unittest.TestCase):
+ 
+@@ -944,7 +944,8 @@
+     local = os.path.join(DATADIR, "example.gtf.gz")
+ 
+     def setUp(self):
+-        self.remote_file = pysam.TabixFile(self.url, "r")
++        if checkURL(self.url):
++            self.remote_file = pysam.TabixFile(self.url, "r")
+         self.local_file = pysam.TabixFile(self.local, "r")
+ 
+     def testFetchAll(self):
+@@ -960,11 +961,12 @@
+ 
+     def testHeader(self):
+         self.assertEqual(list(self.local_file.header), [])
+-        self.assertRaises(AttributeError,
+-                          getattr,
+-                          self.remote_file,
+-                          "header")
+ 
++        if checkURL(self.url):
++            self.assertRaises(AttributeError,
++                              getattr,
++                              self.remote_file,
++                              "header")
+ 
+ class TestIndexArgument(unittest.TestCase):
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 639025c..d7785a3 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,4 @@
 change-htslib-statement-to-link-to-debian
 adding-include-hts-dirs
 ignore-htslib-dir.patch
-strip_online_tests.patch
+disable-tests-requiring-network.patch
diff --git a/debian/patches/strip_online_tests.patch b/debian/patches/strip_online_tests.patch
deleted file mode 100644
index c2bc21f..0000000
--- a/debian/patches/strip_online_tests.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-Author: Andreas Tille <tille@debian.org>
-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