[med-svn] [python-biopython] 02/10: Skip test needing a network connection

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository python-biopython.

commit e17febf6e97dd12d37f16c4c08d80bc2a794d648
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jun 9 09:06:18 2016 +0200

    Skip test needing a network connection
---
 debian/changelog                                   |  3 +-
 debian/patches/series                              |  1 +
 .../skip_test_needing_network_connection.patch     | 66 ++++++++++++++++++++++
 3 files changed, 69 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index 61dfae8..df40eb2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,7 +3,8 @@ python-biopython (1.67+dfsg-1) UNRELEASED; urgency=medium
   * New upstream version
   * Point d/watch to github
   * xz compression in d/watch
-  * Take over patch from upstream to fix detection of rpsblast 
+  * Take over patch from upstream to fix detection of rpsblast
+  * Skip test needing a network connection
 
  -- Andreas Tille <tille at debian.org>  Wed, 08 Jun 2016 21:21:55 +0200
 
diff --git a/debian/patches/series b/debian/patches/series
index cc9705d..4ebd9f0 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@ remove_mathml-qname.patch
 privacy_breach.patch
 fix_test_phyml_tool.patch
 fix_detection_of_rpsblast.patch
+skip_test_needing_network_connection.patch
diff --git a/debian/patches/skip_test_needing_network_connection.patch b/debian/patches/skip_test_needing_network_connection.patch
new file mode 100644
index 0000000..c89211b
--- /dev/null
+++ b/debian/patches/skip_test_needing_network_connection.patch
@@ -0,0 +1,66 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 08 Jun 2016 21:21:55 +0200
+Description: This test requires a working network connection and can not be
+ run in a pbuilder chroot
+
+--- a/Tests/common_BioSQL.py
++++ b/Tests/common_BioSQL.py
+@@ -610,58 +610,6 @@ class LoaderTest(unittest.TestCase):
+                                     'M81224.1', 'X55053.1', 'X62281.1'])
+ 
+ 
+-class TaxonomyTest(unittest.TestCase):
+-    """Test proper insertion and retrieval of taxonomy data
+-    """
+-    def setUp(self):
+-        from Bio import Entrez
+-        Entrez.email = "biopython-dev at biopython.org"
+-        # create TESTDB
+-        create_database()
+-
+-        # load the database
+-        db_name = "biosql-test"
+-        self.server = BioSeqDatabase.open_database(driver=DBDRIVER,
+-                                                   user=DBUSER, passwd=DBPASSWD,
+-                                                   host=DBHOST, db=TESTDB)
+-
+-        # remove the database if it already exists
+-        try:
+-            self.server[db_name]
+-            self.server.remove_database(db_name)
+-        except KeyError:
+-            pass
+-
+-        self.db = self.server.new_database(db_name)
+-
+-        # get the GenBank file we are going to put into it
+-        self.iterator = SeqIO.parse("GenBank/cor6_6.gb", "gb")
+-
+-    def tearDown(self):
+-        self.server.close()
+-        destroy_database()
+-        del self.db
+-        del self.server
+-
+-    def test_taxon_left_right_values(self):
+-        self.db.load(self.iterator, True)
+-        sql = """SELECT DISTINCT include.ncbi_taxon_id FROM taxon
+-                  INNER JOIN taxon AS include ON
+-                      (include.left_value BETWEEN taxon.left_value
+-                                  AND taxon.right_value)
+-                  WHERE taxon.taxon_id IN
+-                      (SELECT taxon_id FROM taxon_name
+-                                  WHERE name = 'Brassicales')
+-                      AND include.right_value - include.left_value = 1"""
+-
+-        rows = self.db.adaptor.execute_and_fetchall(sql)
+-        self.assertEqual(4, len(rows))
+-        values = set()
+-        for row in rows:
+-            values.add(row[0])
+-        self.assertEqual(set([3704, 3711, 3708, 3702]), set(values))
+-
+-
+ class DeleteTest(unittest.TestCase):
+     """Test proper deletion of entries from a database."""
+ 

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-biopython.git