BioSQL updates for python3 (biopython#2654)

mdehoon · web-flow · commit 85e8956832c0 · 2020-02-09T16:54:58.000Z
diff --git a/BioSQL/BioSeq.py b/BioSQL/BioSeq.py
@@ -45,9 +45,6 @@ def __len__(self):
 
     def __getitem__(self, index):  # Seq API requirement
         """Return a subsequence or single letter."""
-        # Note since Python 2.0, __getslice__ is deprecated
-        # and __getitem__ is used instead.
-        # See http://docs.python.org/ref/sequence-methods.html
         if isinstance(index, int):
             # Return a single letter as a string
             i = index
diff --git a/BioSQL/BioSeqDatabase.py b/BioSQL/BioSeqDatabase.py
@@ -213,49 +213,19 @@ def __iter__(self):
         # TODO - Iterate over the cursor, much more efficient
         return iter(self.adaptor.list_biodatabase_names())
 
-    if hasattr(dict, "iteritems"):
-        # Python 2, use iteritems etc
-        def keys(self):
-            """List of namespaces (sub-databases) in the database."""
-            return self.adaptor.list_biodatabase_names()
-
-        def values(self):
-            """List of BioSeqDatabase objects in the database."""
-            return [self[key] for key in self]
-
-        def items(self):
-            """List of (namespace, BioSeqDatabase) for entries in database."""
-            return [(key, self[key]) for key in self]
-
-        def iterkeys(self):
-            """Iterate over namespaces (sub-databases) in the database."""
-            return iter(self)
-
-        def itervalues(self):
-            """Iterate over BioSeqDatabase objects in the database."""
-            for key in self:
-                yield self[key]
-
-        def iteritems(self):
-            """Iterate over (namespace, BioSeqDatabase) in the database."""
-            for key in self:
-                yield key, self[key]
-
-    else:
-        # Python 3, items etc are all iterators
-        def keys(self):
-            """Iterate over namespaces (sub-databases) in the database."""
-            return iter(self)
+    def keys(self):
+        """Iterate over namespaces (sub-databases) in the database."""
+        return iter(self)
 
-        def values(self):
-            """Iterate over BioSeqDatabase objects in the database."""
-            for key in self:
-                yield self[key]
+    def values(self):
+        """Iterate over BioSeqDatabase objects in the database."""
+        for key in self:
+            yield self[key]
 
-        def items(self):
-            """Iterate over (namespace, BioSeqDatabase) in the database."""
-            for key in self:
-                yield key, self[key]
+    def items(self):
+        """Iterate over (namespace, BioSeqDatabase) in the database."""
+        for key in self:
+            yield key, self[key]
 
     def __delitem__(self, name):
         """Remove a namespace and all its entries."""
@@ -832,49 +802,19 @@ def __iter__(self):
         # TODO - Iterate over the cursor, much more efficient
         return iter(self.adaptor.list_bioentry_ids(self.dbid))
 
-    if hasattr(dict, "iteritems"):
-        # Python 2, use iteritems etc
-        def keys(self):
-            """List of ids which may not be meaningful outside this database."""
-            return self.adaptor.list_bioentry_ids(self.dbid)
-
-        def values(self):
-            """List of DBSeqRecord objects in the namespace (sub database)."""
-            return [self[key] for key in self]
-
-        def items(self):
-            """List of (id, DBSeqRecord) for the namespace (sub database)."""
-            return [(key, self[key]) for key in self]
-
-        def iterkeys(self):
-            """Iterate over ids (which may not be meaningful outside this database)."""
-            return iter(self)
-
-        def itervalues(self):
-            """Iterate over DBSeqRecord objects in the namespace (sub database)."""
-            for key in self:
-                yield self[key]
+    def keys(self):
+        """Iterate over ids (which may not be meaningful outside this database)."""
+        return iter(self)
 
-        def iteritems(self):
-            """Iterate over (id, DBSeqRecord) for the namespace (sub database)."""
-            for key in self:
-                yield key, self[key]
+    def values(self):
+        """Iterate over DBSeqRecord objects in the namespace (sub database)."""
+        for key in self:
+            yield self[key]
 
-    else:
-        # Python 3, items etc are all iterators
-        def keys(self):
-            """Iterate over ids (which may not be meaningful outside this database)."""
-            return iter(self)
-
-        def values(self):
-            """Iterate over DBSeqRecord objects in the namespace (sub database)."""
-            for key in self:
-                yield self[key]
-
-        def items(self):
-            """Iterate over (id, DBSeqRecord) for the namespace (sub database)."""
-            for key in self:
-                yield key, self[key]
+    def items(self):
+        """Iterate over (id, DBSeqRecord) for the namespace (sub database)."""
+        for key in self:
+            yield key, self[key]
 
     def lookup(self, **kwargs):
         """Return a DBSeqRecord using an acceptable identifier.
diff --git a/BioSQL/Loader.py b/BioSQL/Loader.py
@@ -1095,7 +1095,7 @@ def _load_seqfeature_dbxref(self, dbxrefs, seqfeature_id):
                 db = dbxref_data[0]
                 accessions = dbxref_data[1:]
             except Exception:
-                raise ValueError("Parsing of db_xref failed: '%s'" % value)
+                raise ValueError("Parsing of db_xref failed: '%s'" % value) from None
             # Loop over all the grabbed accessions, and attempt to fill the
             # table
             for accession in accessions:
@@ -1177,7 +1177,9 @@ def _load_dbxrefs(self, record, bioentry_id):
                 db = db.strip()
                 accession = accession.strip()
             except Exception:
-                raise ValueError("Parsing of dbxrefs list failed: '%s'" % value)
+                raise ValueError(
+                    "Parsing of dbxrefs list failed: '%s'" % value
+                ) from None
             # Get the dbxref_id value for the dbxref data
             dbxref_id = self._get_dbxref_id(db, accession)
             # Insert the bioentry_dbxref  data
diff --git a/Tests/common_BioSQL.py b/Tests/common_BioSQL.py
@@ -94,7 +94,7 @@ def check_config(dbdriver, dbtype, dbhost, dbuser, dbpasswd, testdb):
                 import org.postgresql.Driver
         except ImportError:
             message = "Install the JDBC driver for %s to use BioSQL " % DBTYPE
-            raise MissingExternalDependencyError(message)
+            raise MissingExternalDependencyError(message) from None
     else:
         try:
             __import__(DBDRIVER)
@@ -103,7 +103,7 @@ def check_config(dbdriver, dbtype, dbhost, dbuser, dbpasswd, testdb):
                 message = "Install MySQLdb or mysqlclient if you want to use %s with BioSQL " % (DBTYPE)
             else:
                 message = "Install %s if you want to use %s with BioSQL " % (DBDRIVER, DBTYPE)
-            raise MissingExternalDependencyError(message)
+            raise MissingExternalDependencyError(message) from None
 
     try:
         if DBDRIVER in ["sqlite3"]:
@@ -115,7 +115,7 @@ def check_config(dbdriver, dbtype, dbhost, dbuser, dbpasswd, testdb):
         del server
     except Exception as e:
         message = "Connection failed, check settings if you plan to use BioSQL: %s" % e
-        raise MissingExternalDependencyError(message)
+        raise MissingExternalDependencyError(message) from None
 
     DBSCHEMA = "biosqldb-" + DBTYPE + ".sql"
     SQL_FILE = os.path.join(os.getcwd(), "BioSQL", DBSCHEMA)
@@ -573,7 +573,7 @@ def test_seq_features(self):
             self.assertEqual(cds_feature.qualifiers["codon_start"], ["1"])
         except KeyError:
             raise KeyError("Missing expected entries, have %s"
-                           % repr(cds_feature.qualifiers))
+                           % repr(cds_feature.qualifiers)) from None
 
         self.assertIn("db_xref", cds_feature.qualifiers)
         multi_ann = cds_feature.qualifiers["db_xref"]
@@ -961,9 +961,8 @@ def test_transfer(self):
     def test_reload(self):
         """Make sure can't reimport existing records."""
         gb_file = os.path.join(os.getcwd(), "GenBank", "cor6_6.gb")
-        gb_handle = open(gb_file)
-        record = next(SeqIO.parse(gb_handle, "gb"))
-        gb_handle.close()
+        with open(gb_file) as gb_handle:
+            record = next(SeqIO.parse(gb_handle, "gb"))
         # Should be in database already...
         db_record = self.db.lookup(accession="X55053")
         self.assertEqual(db_record.id, record.id)
