+++ /dev/null
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Wed, 13 Dec 2017 13:03:50 +0100
-Description: Exclude tests trying to access remote http sites and thus need
- to fail in a chroot without network access.
- .
- Remark: Any more elegant method than dumb removal to exclude the tests would
- be welcome.
-
---- a/save/pysam_test2.6.py
-+++ b/save/pysam_test2.6.py
-@@ -1284,61 +1284,6 @@ class TestDoubleFetch(unittest.TestCase)
- samfile1.fetch( until_eof = True )):
- self.assertEqual( a.compare( b), 0 )
-
--class TestRemoteFileFTP(unittest.TestCase):
-- '''test remote access.
--
-- '''
--
-- # Need to find an ftp server without password on standard
-- # port.
--
-- url = "ftp://ftp.sanger.ac.uk/pub/rd/humanSequences/CV.bam"
-- region = "1:1-1000"
--
-- def testFTPView( self ):
-- return
-- result = pysam.view( self.url, self.region )
-- self.assertEqual( len(result), 36 )
--
-- def testFTPFetch( self ):
-- return
-- samfile = pysam.Samfile(self.url, "rb")
-- result = list(samfile.fetch( region = self.region ))
-- 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 = "ex1.bam"
--
-- def testView( self ):
-- samfile_local = pysam.Samfile(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 ):
-- samfile = pysam.Samfile(self.url, "rb")
-- result = list(samfile.fetch( region = self.region ))
-- samfile_local = pysam.Samfile(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 ):
-- samfile = pysam.Samfile(self.url, "rb")
-- result = list(samfile.fetch())
-- samfile_local = pysam.Samfile(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/AlignmentFile_test.py
-+++ b/tests/AlignmentFile_test.py
-@@ -1559,81 +1559,6 @@ class TestDoubleFetchCRAMWithReference(T
- reference_filename = os.path.join(BAM_DATADIR, 'ex1.fa')
-
-
--class TestRemoteFileFTP(unittest.TestCase):
--
-- '''test remote access.
--
-- '''
--
-- # Need to find an ftp server without password on standard
-- # port.
--
-- url = "ftp://ftp.sanger.ac.uk/pub/rd/humanSequences/CV.bam"
-- region = "1:1-1000"
--
-- def testFTPView(self):
-- return
-- if not checkURL(self.url):
-- return
--
-- result = pysam.samtools.view(self.url, self.region)
-- self.assertEqual(len(result), 36)
--
-- def testFTPFetch(self):
-- return
-- if not checkURL(self.url):
-- return
--
-- samfile = pysam.AlignmentFile(self.url, "rb")
-- result = list(samfile.fetch(region=self.region))
-- 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(BAM_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.samtools.view(self.url, self.region)
-- self.assertEqual(len(result.splitlines()), len(ref))
--
-- def testFetch(self):
-- if not checkURL(self.url):
-- return
--
-- with pysam.AlignmentFile(self.url, "rb") as samfile:
-- result = list(samfile.fetch(region=self.region))
--
-- with pysam.AlignmentFile(self.local, "rb") as samfile_local:
-- 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
--
-- with pysam.AlignmentFile(self.url, "rb") as samfile:
-- result = list(samfile.fetch())
--
-- with pysam.AlignmentFile(self.local, "rb") as samfile_local:
-- 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
-@@ -1039,66 +1039,6 @@ for vcf_file in vcf_files:
- globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))
-
-
--class TestRemoteFileHTTP(unittest.TestCase):
--
-- url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz"
-- region = "chr1:1-1000"
-- local = os.path.join(TABIX_DATADIR, "example.gtf.gz")
--
-- def setUp(self):
-- if not pysam.config.HAVE_LIBCURL or not checkURL(self.url):
-- self.remote_file = None
-- else:
-- self.remote_file = pysam.TabixFile(self.url, "r")
--
-- self.local_file = pysam.TabixFile(self.local, "r")
--
-- def tearDown(self):
-- if self.remote_file is None:
-- return
--
-- self.remote_file.close()
-- self.local_file.close()
--
-- def testFetchAll(self):
-- if self.remote_file is None:
-- return
--
-- remote_result = list(self.remote_file.fetch())
-- local_result = list(self.local_file.fetch())
--
-- self.assertEqual(len(remote_result), len(local_result))
-- for x, y in zip(remote_result, local_result):
-- self.assertEqual(x, y)
--
-- def testHeader(self):
-- if self.remote_file is None:
-- return
--
-- 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 pysam.config.HAVE_LIBCURL or not checkURL(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):
-
- filename_src = os.path.join(TABIX_DATADIR, "example.vcf.gz")
projects / python-pysam.git / commitdiff