Python safe_md5 Examples

Example #1

File: test_init.py Project: gregcaporaso/qiime-default-reference

 def test_get_template_alignment_column_mask(self):
     # make sure the literal Lane mask matches the real file's MD5 (without
     # the trailing newline)
     exp = 'e3e5f2804e29694e03a01fd9cc157a53'
     obs = safe_md5(
         StringIO(get_template_alignment_column_mask())).hexdigest()
     self.assertEqual(obs, exp)

Example #2

File: test_init.py Project: linls1912/qiime-default-reference

 def test_get_template_alignment_column_mask(self):
     # make sure the literal Lane mask matches the real file's MD5 (without
     # the trailing newline)
     exp = 'e3e5f2804e29694e03a01fd9cc157a53'
     obs = safe_md5(BytesIO(
         get_template_alignment_column_mask())).hexdigest()
     self.assertEqual(obs, exp)

Example #3

File: test_init.py Project: gregcaporaso/qiime-default-reference

    def test_get_reference_taxonomy(self):
        fp = get_reference_taxonomy()
        self.assertIn(
            os.path.join('gg_13_8_otus', 'taxonomy', '97_otu_taxonomy.txt'), fp)
        self.assertTrue(os.path.isfile(fp))
        self.assertTrue(os.path.isabs(fp))

        with open(fp, 'rb') as f:
            md5 = safe_md5(f).hexdigest()
        self.assertEqual(md5, '56ef15dccf2e931ec173f4f977ed649b')

Example #4

File: test_init.py Project: gregcaporaso/qiime-default-reference

    def test_get_reference_sequences(self):
        fp = get_reference_sequences()
        self.assertIn(
            os.path.join('gg_13_8_otus', 'rep_set', '97_otus.fasta'), fp)
        self.assertTrue(os.path.isfile(fp))
        self.assertTrue(os.path.isabs(fp))

        with open(fp, 'rb') as f:
            md5 = safe_md5(f).hexdigest()
        self.assertEqual(md5, '50b2269712b3738afb41892bed936c29')

Example #5

File: test_init.py Project: linls1912/qiime-default-reference

    def test_get_reference_tree(self):
        fp = get_reference_tree()
        self.assertIn(os.path.join('gg_13_8_otus', 'trees', '97_otus.tree'),
                      fp)
        self.assertTrue(os.path.isfile(fp))
        self.assertTrue(os.path.isabs(fp))

        with open(fp, 'rb') as f:
            md5 = safe_md5(f).hexdigest()
        self.assertEqual(md5, 'b7e76593bce82913af1cfb06edf15732')

Example #6

File: test_init.py Project: linls1912/qiime-default-reference

    def test_get_reference_sequences(self):
        fp = get_reference_sequences()
        self.assertIn(os.path.join('gg_13_8_otus', 'rep_set', '97_otus.fasta'),
                      fp)
        self.assertTrue(os.path.isfile(fp))
        self.assertTrue(os.path.isabs(fp))

        with open(fp, 'rb') as f:
            md5 = safe_md5(f).hexdigest()
        self.assertEqual(md5, '50b2269712b3738afb41892bed936c29')

Example #7

File: test_init.py Project: biocore/qiime-default-reference

    def test_get_reference_tree(self):
        fp = get_reference_tree()
        self.assertIn(
            os.path.join('gg_13_8_otus', 'trees', '97_otus.tree'), fp)
        self.assertTrue(os.path.isfile(fp))
        self.assertTrue(os.path.isabs(fp))

        with open(fp, 'rb') as f:
            md5 = safe_md5(f).hexdigest()
        self.assertEqual(md5, 'b7e76593bce82913af1cfb06edf15732')

Example #8

File: test_init.py Project: gregcaporaso/qiime-default-reference

    def test_get_template_alignment(self):
        fp = get_template_alignment()
        self.assertIn(
            os.path.join('gg_13_8_otus', 'rep_set_aligned', '85_otus.fasta'),
            fp)
        self.assertTrue(os.path.isfile(fp))
        self.assertTrue(os.path.isabs(fp))

        with open(fp, 'rb') as f:
            md5 = safe_md5(f).hexdigest()
        self.assertEqual(md5, 'd85dcad4c62e22305e412c1be2f25987')

Example #9

File: test_init.py Project: linls1912/qiime-default-reference

    def test_get_template_alignment(self):
        fp = get_template_alignment()
        self.assertIn(
            os.path.join('gg_13_8_otus', 'rep_set_aligned',
                         '85_otus.pynast.fasta'), fp)
        self.assertTrue(os.path.isfile(fp))
        self.assertTrue(os.path.isabs(fp))

        with open(fp, 'rb') as f:
            md5 = safe_md5(f).hexdigest()
        self.assertEqual(md5, '1de2e593b38041c5b3012220325b76fa')

Example #10

File: test_init.py Project: linls1912/qiime-default-reference

    def test_get_reference_taxonomy(self):
        fp = get_reference_taxonomy()
        self.assertIn(
            os.path.join('gg_13_8_otus', 'taxonomy', '97_otu_taxonomy.txt'),
            fp)
        self.assertTrue(os.path.isfile(fp))
        self.assertTrue(os.path.isabs(fp))

        with open(fp, 'rb') as f:
            md5 = safe_md5(f).hexdigest()
        self.assertEqual(md5, '56ef15dccf2e931ec173f4f977ed649b')

Example #11

File: test_init.py Project: biocore/qiime-default-reference

    def test_get_template_alignment(self):
        fp = get_template_alignment()
        self.assertIn(
            os.path.join('gg_13_8_otus', 'rep_set_aligned', '85_otus.pynast.fasta'),
            fp)
        self.assertTrue(os.path.isfile(fp))
        self.assertTrue(os.path.isabs(fp))

        with open(fp, 'rb') as f:
            md5 = safe_md5(f).hexdigest()
        self.assertEqual(md5, '1de2e593b38041c5b3012220325b76fa')

Example #12

File: test_init.py Project: gregcaporaso/qiime-default-reference

 def test_safe_md5(self):
     exp = 'ab07acbb1e496801937adfa772424bf7'
     fd = StringIO(b'foo bar baz')
     obs = safe_md5(fd)
     self.assertEqual(obs.hexdigest(), exp)
     fd.close()

Example #13

File: test_init.py Project: linls1912/qiime-default-reference

 def test_safe_md5(self):
     exp = 'ab07acbb1e496801937adfa772424bf7'
     fd = BytesIO(b'foo bar baz')
     obs = safe_md5(fd)
     self.assertEqual(obs.hexdigest(), exp)
     fd.close()