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Author: Andreas Tille <tille@debian.org>
Last-Update: 2018-09-11
Description: Skip tests trying to access remote site
Forwarded: not-needed
--- python-pysam.orig/tests/AlignmentFile_test.py
+++ python-pysam/tests/AlignmentFile_test.py
@@ -497,17 +497,6 @@
"tmp_ex2.sam",
"rb", "wh")
- def testBAM2CRAM(self):
- # ignore header (md5 sum)
- self.checkEcho("ex2.bam",
- "ex2.cram",
- "tmp_ex2.cram",
- "rb", "wc",
- sequence_filename=os.path.join(BAM_DATADIR, "ex1.fa"),
- checkf=partial(
- check_samtools_view_equal,
- without_header=True))
-
def testCRAM2BAM(self):
# ignore header (md5 sum)
self.checkEcho("ex2.cram",
@@ -1633,6 +1622,7 @@
reference_filename = os.path.join(BAM_DATADIR, 'ex1.fa')
+@unittest.skip
class TestRemoteFileFTP(unittest.TestCase):
'''test remote access.
--- python-pysam.orig/tests/tabix_test.py
+++ python-pysam/tests/tabix_test.py
@@ -1013,6 +1013,7 @@
globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))
+@unittest.skip
class TestRemoteFileHTTP(unittest.TestCase):
url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz"
@@ -1052,25 +1053,28 @@
self.assertEqual(list(self.local_file.header), [])
-class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):
-
- url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz"
- region = "chr1:1-1000"
- local = os.path.join(TABIX_DATADIR, "example_comments.gtf.gz")
-
- def setUp(self):
- if not getattr(pysam.config, "HAVE_LIBCURL", 0) or not check_url(self.url):
- self.remote_file = None
- else:
- self.remote_file = pysam.TabixFile(self.url, "r")
- self.local_file = pysam.TabixFile(self.local, "r")
-
- def testHeader(self):
- if self.remote_file is None:
- return
-
- self.assertEqual(list(self.local_file.header), ["# comment at start"])
- self.assertEqual(list(self.local_file.header), self.remote_file.header)
+#@unittest.skip # this leads to
+ # E TypeError: Error when calling the metaclass bases
+ # E function() argument 1 must be code, not str
+#class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):
+#
+# url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz"
+# region = "chr1:1-1000"
+# local = os.path.join(TABIX_DATADIR, "example_comments.gtf.gz")
+#
+# def setUp(self):
+# if not getattr(pysam.config, "HAVE_LIBCURL", 0) or not check_url(self.url):
+# self.remote_file = None
+# else:
+# self.remote_file = pysam.TabixFile(self.url, "r")
+# self.local_file = pysam.TabixFile(self.local, "r")
+#
+# def testHeader(self):
+# if self.remote_file is None:
+# return
+#
+# self.assertEqual(list(self.local_file.header), ["# comment at start"])
+# self.assertEqual(list(self.local_file.header), self.remote_file.header)
class TestIndexArgument(unittest.TestCase):
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