[med-svn] [python-biopython] 01/04: Add patch from upstream fixing #824048

[Andreas Tille]

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commit 8ac14ce2b5153a3ec33307ca0f7fe78fded6e049
Author: Andreas Tille <tille at debian.org>
Date:   Thu May 19 16:45:26 2016 +0200

    Add patch from upstream fixing #824048
---
 debian/patches/fix_test_NCBI_BLAST_tools.patch | 32 ++++++++++++++++++++++++++
 debian/patches/series                          |  1 +
 2 files changed, 33 insertions(+)

diff --git a/debian/patches/fix_test_NCBI_BLAST_tools.patch b/debian/patches/fix_test_NCBI_BLAST_tools.patch
new file mode 100644
index 0000000..96478c3
--- /dev/null
+++ b/debian/patches/fix_test_NCBI_BLAST_tools.patch
@@ -0,0 +1,32 @@
+Author: Peter Cock <p.j.a.cock at googlemail.com>
+Bug-Debian: https://bugs.debian.org/824048
+Upstream: https://github.com/biopython/biopython/issues/827
+Last-Update: Thu, 19 May 2016 12:32:17 +0100
+Description: sanity test which failed due to a change in the NCBI output
+
+--- a/Tests/test_NCBI_BLAST_tools.py
++++ b/Tests/test_NCBI_BLAST_tools.py
+@@ -100,12 +100,18 @@ class Pairwise(unittest.TestCase):
+         return_code = child.returncode
+         self.assertEqual(return_code, 0, "Got error code %i back from:\n%s"
+                          % (return_code, cline))
+-        self.assertEqual(10, stdoutdata.count("Query= "))
+-        if stdoutdata.count("***** No hits found *****") == 7:
+-            # This happens with BLAST 2.2.26+ which is potentially a bug
+-            pass
++        # Used to get 10 matches from 10 pairwise searches,
++        # as of NCBI BLAST+ 2.3.0 only get 1 Query= line:
++        if stdoutdata.count("Query= ") == 10:
++            if stdoutdata.count("***** No hits found *****") == 7:
++                # This happens with BLAST 2.2.26+ which is potentially a bug
++                pass
++            else:
++                self.assertEqual(9, stdoutdata.count("***** No hits found *****"))
+         else:
+-            self.assertEqual(9, stdoutdata.count("***** No hits found *****"))
++            # Assume this is NCBI BLAST+ 2.3.0 or later,
++            self.assertEqual(1, stdoutdata.count("Query= "))
++            self.assertEqual(0, stdoutdata.count("***** No hits found *****"))
+ 
+         # TODO - Parse it? I think we'd need to update this obsole code :(
+         # records = list(NCBIStandalone.Iterator(StringIO(stdoutdata),
diff --git a/debian/patches/series b/debian/patches/series
index 60dbfde..85da082 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 remove_mathml-qname.patch
 privacy_breach.patch
 fix_test_phyml_tool.patch
+fix_test_NCBI_BLAST_tools.patch

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