From 7846d7fe9a73cb060e6a8c2adc01f62878d9929f Mon Sep 17 00:00:00 2001 From: Afif Elghraoui Date: Sun, 22 Apr 2018 18:36:25 -0400 Subject: [PATCH] Update patches --- .../exclude_tests_accessing_remote_http.patch | 225 ------------------ debian/patches/series | 1 - .../skip_test_needing_missing_data.patch | 12 +- 3 files changed, 6 insertions(+), 232 deletions(-) delete mode 100644 debian/patches/exclude_tests_accessing_remote_http.patch diff --git a/debian/patches/exclude_tests_accessing_remote_http.patch b/debian/patches/exclude_tests_accessing_remote_http.patch deleted file mode 100644 index 6f5fa65..0000000 --- a/debian/patches/exclude_tests_accessing_remote_http.patch +++ /dev/null @@ -1,225 +0,0 @@ -Author: Andreas Tille -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") diff --git a/debian/patches/series b/debian/patches/series index 97110d9..881b73d 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,4 +1,3 @@ execute-linking-tests-only-when-explicitely-reque.patch xfail.patch -exclude_tests_accessing_remote_http.patch skip_test_needing_missing_data.patch diff --git a/debian/patches/skip_test_needing_missing_data.patch b/debian/patches/skip_test_needing_missing_data.patch index 689f5ff..9673e16 100644 --- a/debian/patches/skip_test_needing_missing_data.patch +++ b/debian/patches/skip_test_needing_missing_data.patch @@ -4,9 +4,9 @@ Author: Andreas Tille Last-Update: Sat, 17 Feb 2018 15:24:34 +0100 Forwarded: https://github.com/pysam-developers/pysam/issues/626 ---- a/tests/pysam_data/Makefile -+++ b/tests/pysam_data/Makefile -@@ -20,8 +20,7 @@ all: ex1.pileup.gz \ +--- python-pysam.orig/tests/pysam_data/Makefile ++++ python-pysam/tests/pysam_data/Makefile +@@ -20,8 +20,7 @@ explicit_index.bam explicit_index.cram \ faidx_empty_seq.fq.gz \ ex1.fa.gz ex1.fa.gz.csi \ @@ -16,9 +16,9 @@ Forwarded: https://github.com/pysam-developers/pysam/issues/626 # ex2.sam - as ex1.sam, but with header ex2.sam.gz: ex1.bam ex1.bam.bai ---- a/tests/AlignmentFile_test.py -+++ b/tests/AlignmentFile_test.py -@@ -1361,12 +1361,7 @@ class TestEmptyHeader(unittest.TestCase) +--- python-pysam.orig/tests/AlignmentFile_test.py ++++ python-pysam/tests/AlignmentFile_test.py +@@ -1359,12 +1359,7 @@ 'example_empty_header.bam')) self.assertEqual(s.header.to_dict(), {'SQ': [{'LN': 1000, 'SN': 'chr1'}]}) -- 2.30.2