Remove obsolete Db module

Now that we ported the database to SQLAlchemy, we remove the obsolete Db
module and all references to it.

mutalyzer/Db.py

-#!/usr/bin/python
-
-"""
-Module for database access.
-The Db class is a superclass of the rest of the classes and should not be
-used as such. The superclass mainly consists of a wrapper for SQL
-statements.
-
-@requires: MySQLdb
-@requires: types
-@requires: time
-@requires: os
-"""
-
-#Public classes:
-#    - Db      ; Log in to a database and keep it open for queries.
-#    - Mapping ; Mapping of transcripts and genes.
-#    - Cache   ; Cache administration.
-#    - Batch   ; Batch checker.
-
-
-import types
-import warnings
-
-import MySQLdb
-
-from mutalyzer import util
-from mutalyzer.config import settings
-
-
-#
-# Note that compound queries are split into single queries because of a bug
-# in MySQLdb. The functions load_Update(),  merge_cdsUpdates() and
-# merge_Update (search for MYSQL_BUG in this file) are affected and may be
-# rewritten when this bug is fixed.
-#
-
-class Db():
-    """
-    Query the database server (and lazily keep a connection open to it).
-
-    This class is subclassed below to create specific interfaces to the
-    database.
-    """
-    def __init__(self, database, user, host):
-        """
-        Create an interface to the database.
-
-        @arg database: Name of the database to use.
-        @type database: str
-        @arg user: User name for the database.
-        @type user: str
-        @arg host: Host name for the database.
-        @type host: str
-        """
-        self._database = database
-        self._user = user
-        self._host = host
-
-        # The connection to the database server is created lazily in the query
-        # method.
-        self._connection = None
-    #__init__
-
-    def _connect(self):
-        """
-        Connect to the database server.
-
-        Note: We would like to automatically reconnect to the database server.
-            This is especially useful for long-running processes such as the
-            batch deamon, which would otherwise loose their connection on an
-            event such as restarting the database server.
-            The MySQL client libraries provide a reconnect option, but this
-            is unfortunately not implemented in (most versions of) the Python
-            MySQLdb module.
-            Therefore we manually implement automatic reconnects in the query
-            method.
-            Also see Trac ticket #91.
-        """
-        self._connection = MySQLdb.connect(
-                user=self._user, db=self._database, host=self._host)
-    #_connect
-
-    def query(self, statement):
-        """
-        Query the database.
-
-        @arg statement: The statement that is to be queried
-        @type statement: tuple (string, (args))
-
-        @return: The result of the query
-        @rtype: list
-        """
-
-        # Convert the arguments to a tuple.
-        if type(statement[1]) != types.TupleType :
-            args = statement[1],
-        else :
-            args = statement[1]
-
-        # Escape the input to prevent SQL injections.
-        escaped_args = []
-        if args != (None,) : # Don't escape the empty string.
-            for i in args :
-                if i :
-                    if type(i) in [types.StringType, types.UnicodeType]:
-                        escaped_args.append(MySQLdb.escape_string(str(i)))
-                    else :
-                        escaped_args.append(i)
-                else :
-                    escaped_args.append(None)
-        #if
-
-        # Do the query, but first connect to the database server if needed.
-        # This makes sure lost connections are re-created automatically (e.g.
-        # in case the server was restarted for maintenance).
-        try:
-            cursor = self._connection.cursor()
-            cursor.execute(statement[0], tuple(escaped_args))
-        except (AttributeError, MySQLdb.OperationalError):
-            self._connect()
-            cursor = self._connection.cursor()
-            cursor.execute(statement[0], tuple(escaped_args))
-
-        result = cursor.fetchall()
-        cursor.close()
-
-        return result
-    #query
-#Db

mutalyzer/GenRecord.py

@@ -6,7 +6,6 @@ search for them each time.
 
 @requires: Crossmap
 @requires: Bio
-@requires: Db
 """
 # Public classes:
 #     - PList     ; Store a general location and a list of splice sites.
@@ -20,7 +19,6 @@ import Bio
 
 from mutalyzer import util
 from mutalyzer import Crossmap
-from mutalyzer import Db
 
 
 SPLICE_ALARM = 2

mutalyzer/Retriever.py

@@ -63,13 +63,7 @@ class Retriever(object) :
         - uploadrecord(raw_data) ; Let someone upload a GenBank file.
         - loadrecord(identifier) ; Load a record, store it in the cache, manage
         the cache and return the record.
-
-    Inherited methods from Db.Output:
-        - WarningMsg(filename, message) ; Print a warning message.
-        - ErrorMsg(filename, message)   ; Print an error message and log it.
-        - LogMsg(filename, message)     ; Log a message.
     """
-
     def __init__(self, output) :
         """
         Use variables from the configuration file for some simple

mutalyzer/config/default_settings.py

@@ -33,15 +33,6 @@ REDIS_URI = None
 # Database connection URI (can be any SQLAlchemy connection URI).
 DATABASE_URI = 'sqlite://'
 
-# Host name for local MySQL databases.
-MYSQL_HOST = 'localhost'
-
-# User for local MySQL databases.
-MYSQL_USER = 'mutalyzer'
-
-# Local MySQL database name.
-MYSQL_DATABASE = 'mutalyzer'
-
 # Default genome assembly (by name or alias).
 DEFAULT_ASSEMBLY = 'hg19'
 

mutalyzer/mapping.py

@@ -18,7 +18,6 @@ import MySQLdb
 
 from mutalyzer.db.models import Chromosome, TranscriptMapping
 from mutalyzer.grammar import Grammar
-from mutalyzer import Db
 from mutalyzer import Crossmap
 from mutalyzer import Retriever
 from mutalyzer.models import SoapMessage, Mapping, Transcript

mutalyzer/services/rpc.py

@@ -30,7 +30,6 @@ from mutalyzer.grammar import Grammar
 from mutalyzer.sync import CacheSync
 from mutalyzer import stats
 from mutalyzer import variantchecker
-from mutalyzer import Db
 from mutalyzer.mapping import Converter
 from mutalyzer import File
 from mutalyzer import Retriever

mutalyzer/website.py

@@ -42,7 +42,6 @@ from mutalyzer.services import soap
 from mutalyzer import variantchecker
 from mutalyzer.output import Output
 from mutalyzer.mapping import Converter
-from mutalyzer import Db
 from mutalyzer import Scheduler
 from mutalyzer import Retriever
 from mutalyzer import File

tests/test_services_soap.py

@@ -15,7 +15,6 @@ from spyne.model.fault import Fault
 from suds.client import Client
 
 import mutalyzer
-from mutalyzer import Db
 from mutalyzer.output import Output
 from mutalyzer.services.soap import application
 from mutalyzer.sync import CacheSync