From 667f39a697140c95fefa53e9f559cef9e4d2feeb Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Fri, 10 Jan 2014 12:46:00 +0100
Subject: [PATCH] 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 | 130 ---------------------------
mutalyzer/GenRecord.py | 2 -
mutalyzer/Retriever.py | 6 --
mutalyzer/config/default_settings.py | 9 --
mutalyzer/mapping.py | 1 -
mutalyzer/services/rpc.py | 1 -
mutalyzer/website.py | 1 -
tests/test_services_soap.py | 1 -
8 files changed, 151 deletions(-)
delete mode 100644 mutalyzer/Db.py
diff --git a/mutalyzer/Db.py b/mutalyzer/Db.py
deleted file mode 100644
index 376221d6..00000000
--- a/mutalyzer/Db.py
+++ /dev/null
@@ -1,130 +0,0 @@
-#!/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
diff --git a/mutalyzer/GenRecord.py b/mutalyzer/GenRecord.py
index 917d056c..b30ed800 100644
--- a/mutalyzer/GenRecord.py
+++ b/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
diff --git a/mutalyzer/Retriever.py b/mutalyzer/Retriever.py
index 7c224e48..d2d01c5d 100644
--- a/mutalyzer/Retriever.py
+++ b/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
diff --git a/mutalyzer/config/default_settings.py b/mutalyzer/config/default_settings.py
index 108ad84d..d7cd7457 100644
--- a/mutalyzer/config/default_settings.py
+++ b/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'
diff --git a/mutalyzer/mapping.py b/mutalyzer/mapping.py
index c10c1545..7bc9813b 100644
--- a/mutalyzer/mapping.py
+++ b/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
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index 86cc0a16..ced3405e 100644
--- a/mutalyzer/services/rpc.py
+++ b/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
diff --git a/mutalyzer/website.py b/mutalyzer/website.py
index 63dd3247..266185fd 100644
--- a/mutalyzer/website.py
+++ b/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
diff --git a/tests/test_services_soap.py b/tests/test_services_soap.py
index ed5b3e6b..13d0335c 100644
--- a/tests/test_services_soap.py
+++ b/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
--
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