Fixes broken tests:

 - mikado.db was missing orf names
 - pandas is returning UnicodeDecodeError instead of ValueError or ParserError when attempting to process a .h5 file

Summary:
Mikado was not correctly storing the orf names in the DB which meant nodes in the clique graph were being created with "None", the behaviour for handling None as node name was changed in networkx triggering the underlying Mikado issue. (See networkx/networkx#4892)

Mikado/serializers/external.py

@@ -162,7 +162,7 @@ def __init__(self, handle,
 
         try:
             self.data = pd.read_csv(self.handle, delimiter=delimiter, index_col=["tid"])
-        except (ValueError, pd.errors.ParserError) as exc:
+        except (ValueError, pd.errors.ParserError, UnicodeDecodeError) as exc:
             self.logger.critical("Invalid input file!")
             self.logger.critical(exc)
             raise

Mikado/tests/test_db_utils.py

@@ -43,13 +43,13 @@ def test_content(self):
         sessionmaker = sqlalchemy.orm.sessionmaker(bind=engine)
         session = sessionmaker()
         # Simple tests based on the static content of the dictionary
-        self.assertEqual(session.query(serializers.junction.Junction).count(), 372,
+        self.assertEqual(session.query(serializers.junction.Junction).count(), 371,
                          self.json.db_settings)
-        self.assertEqual(session.query(serializers.orf.Orf).count(), 169)
-        self.assertEqual(session.query(serializers.blast_serializer.Target).count(), 38909)
-        self.assertEqual(session.query(serializers.blast_serializer.Query).count(), 93)
-        self.assertEqual(session.query(serializers.blast_serializer.Hit).count(), 5034)
-        self.assertEqual(session.query(serializers.blast_serializer.Hsp).count(), 13585)
+        self.assertEqual(session.query(serializers.orf.Orf).count(), 268)
+        self.assertEqual(session.query(serializers.blast_serializer.Target).count(), 42992)
+        self.assertEqual(session.query(serializers.blast_serializer.Query).count(), 112)
+        self.assertEqual(session.query(serializers.blast_serializer.Hit).count(), 674)
+        self.assertEqual(session.query(serializers.blast_serializer.Hsp).count(), 674)
 
         first_query = session.query(serializers.blast_serializer.Query).limit(1).one()
         astup = first_query.as_tuple()

Mikado/tests/test_external_scores.py

@@ -83,7 +83,7 @@ def test_invalid_tsv(self):
                         conf.serialise.files.transcripts)
         logger = create_default_logger("test_no_fasta", level="DEBUG")
         h5 = pkg_resources.resource_filename("Mikado.tests", os.path.join("test_external", "abundance.h5"))
-        with self.assertRaises((pd.errors.ParserError,)):
+        with self.assertRaises((pd.errors.ParserError, UnicodeDecodeError)):
             ExternalSerializer(logger=logger, configuration=conf, handle=h5)
         wrong_tsv_one = pkg_resources.resource_filename("Mikado.tests", os.path.join("test_external", "wrong_1.tsv"))
         with self.assertRaises((ValueError, pd.errors.ParserError)), \