--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/BioSQL/DBUtils.py	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,155 @@
+# Copyright 2002 by Andrew Dalke.  All rights reserved.
+# Revisions 2007-2010 copyright by Peter Cock.  All rights reserved.
+# Revisions 2009 copyright by Brad Chapman.  All rights reserved.
+# Revisions 2013 copyright by Tiago Antao.  All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+#
+# Note that BioSQL (including the database schema and scripts) is
+# available and licensed separately.  Please consult www.biosql.org
+"""Helper code for Biopython's BioSQL code (for internal use)."""
+
+import os
+from typing import Dict, Type
+
+
+_dbutils: Dict[str, Type["Generic_dbutils"]] = {}
+
+
+class Generic_dbutils:
+    """Default database utilities."""
+
+    def __init__(self):
+        """Create a Generic_dbutils object."""
+
+    def tname(self, table):
+        """Return the name of the table."""
+        if table != "biosequence":
+            return table
+        else:
+            return "bioentry"
+
+    def last_id(self, cursor, table):
+        """Return the last used id for a table."""
+        # XXX: Unsafe without transactions isolation
+        table = self.tname(table)
+        sql = f"select max({table}_id) from {table}"
+        cursor.execute(sql)
+        rv = cursor.fetchone()
+        return rv[0]
+
+    def execute(self, cursor, sql, args=None):
+        """Just execute an sql command."""
+        cursor.execute(sql, args or ())
+
+    def executemany(self, cursor, sql, seq):
+        """Execute many sql commands."""
+        cursor.executemany(sql, seq)
+
+    def autocommit(self, conn, y=1):
+        """Set autocommit on the database connection."""
+        # Let's hope it was not really needed
+
+
+class Sqlite_dbutils(Generic_dbutils):
+    """Custom database utilities for SQLite."""
+
+    def _sub_placeholder(self, sql):
+        """Format the argument placeholders for sqlite (PRIVATE)."""
+        return sql.replace("%s", "?")
+
+    def execute(self, cursor, sql, args=None):
+        """Execute SQL command.
+
+        Replaces %s with ? for variable substitution in sqlite3.
+        """
+        sql = self._sub_placeholder(sql)
+        cursor.execute(sql, args or ())
+
+    def executemany(self, cursor, sql, seq):
+        """Execute many sql statements."""
+        sql = self._sub_placeholder(sql)
+        cursor.executemany(sql, seq)
+
+
+_dbutils["sqlite3"] = Sqlite_dbutils
+
+
+class Mysql_dbutils(Generic_dbutils):
+    """Custom database utilities for MySQL."""
+
+    def last_id(self, cursor, table):
+        """Return the last used id for a table."""
+        if os.name == "java":
+            return Generic_dbutils.last_id(self, cursor, table)
+        try:
+            # This worked on older versions of MySQL
+            return cursor.insert_id()
+        except AttributeError:
+            # See bug 2390
+            # Google suggests this is the new way,
+            # same fix also suggested by Eric Gibert:
+            return cursor.lastrowid
+
+
+_dbutils["MySQLdb"] = Mysql_dbutils
+
+
+class _PostgreSQL_dbutils(Generic_dbutils):
+    """Base class for any PostgreSQL adaptor."""
+
+    def next_id(self, cursor, table):
+        table = self.tname(table)
+        sql = f"SELECT nextval('{table}_pk_seq')"
+        cursor.execute(sql)
+        rv = cursor.fetchone()
+        return rv[0]
+
+    def last_id(self, cursor, table):
+        table = self.tname(table)
+        sql = f"SELECT currval('{table}_pk_seq')"
+        cursor.execute(sql)
+        rv = cursor.fetchone()
+        return rv[0]
+
+
+class Psycopg2_dbutils(_PostgreSQL_dbutils):
+    """Custom database utilities for Psycopg2 (PostgreSQL)."""
+
+    def autocommit(self, conn, y=True):
+        """Set autocommit on the database connection."""
+        if y:
+            if os.name == "java":
+                conn.autocommit = 1
+            else:
+                conn.set_isolation_level(0)
+        else:
+            if os.name == "java":
+                conn.autocommit = 0
+            else:
+                conn.set_isolation_level(1)
+
+
+_dbutils["psycopg2"] = Psycopg2_dbutils
+
+
+class Pgdb_dbutils(_PostgreSQL_dbutils):
+    """Custom database utilities for Pgdb (aka PyGreSQL, for PostgreSQL)."""
+
+    def autocommit(self, conn, y=True):
+        """Set autocommit on the database connection. Currently not implemented."""
+        raise NotImplementedError("pgdb does not support this!")
+
+
+_dbutils["pgdb"] = Pgdb_dbutils
+
+
+def get_dbutils(module_name):
+    """Return the correct dbutils object for the database driver."""
+    try:
+        return _dbutils[module_name]()
+    except KeyError:
+        return Generic_dbutils()