add column to SQLAlchemy Table - python

I made a table using SQLAlchemy and forgot to add a column. I basically want to do this:
users.addColumn('user_id', ForeignKey('users.user_id'))
What's the syntax for this? I couldn't find it in the docs.

I have the same problem, and a thought of using migration library only for this trivial thing makes me
tremble. Anyway, this is my attempt so far:
def add_column(engine, table_name, column):
column_name = column.compile(dialect=engine.dialect)
column_type = column.type.compile(engine.dialect)
engine.execute('ALTER TABLE %s ADD COLUMN %s %s' % (table_name, column_name, column_type))
column = Column('new_column_name', String(100), primary_key=True)
add_column(engine, table_name, column)
Still, I don't know how to insert primary_key=True into raw SQL request.

This is referred to as database migration (SQLAlchemy doesn't support migration out of the box). You can look at using sqlalchemy-migrate to help in these kinds of situations, or you can just ALTER TABLE through your chosen database's command line utility,

See this section of the SQLAlchemy documentation: http://docs.sqlalchemy.org/en/latest/core/metadata.html#altering-schemas-through-migrations
Alembic is the latest software to offer this type of functionality and is made by the same author as SQLAlchemy.

I have a database called "ncaaf.db" built with sqlite3 and a table called "games". So I would CD into the same directory on my linux command prompt and do
sqlite3 ncaaf.db
alter table games add column q4 type float
and that is all it takes! Just make sure you update your definitions in your sqlalchemy code.

from sqlalchemy import create_engine
engine = create_engine('sqlite:///db.sqlite3')
engine.execute('alter table table_name add column column_name String')

I had the same problem, I ended up just writing my own function in raw sql. If you are using SQLITE3 this might be useful.
Then if you add the column to your class definition at the same time it seems to do the trick.
import sqlite3
def add_column(database_name, table_name, column_name, data_type):
connection = sqlite3.connect(database_name)
cursor = connection.cursor()
if data_type == "Integer":
data_type_formatted = "INTEGER"
elif data_type == "String":
data_type_formatted = "VARCHAR(100)"
base_command = ("ALTER TABLE '{table_name}' ADD column '{column_name}' '{data_type}'")
sql_command = base_command.format(table_name=table_name, column_name=column_name, data_type=data_type_formatted)
cursor.execute(sql_command)
connection.commit()
connection.close()

I've recently had this same issue so I took a point from AlexP in an earlier answer. The problem was in getting the new column into my program's metadata. Using sqlAlchemy's append_column functionality had some unexpected downstream effects ('str' object has no attribute 'dialect impl'). I corrected this by adding the column with DDL (MySQL database in this case) and then reflecting the table back from the DB into my metadata.
Code is as roughly as follows (modified slightly from what I have in order to reduce it to its minimal essence. I apologize for any mistakes - if there, they should be minor)...
try:
# Use back quotes as a protection against SQL Injection Attacks. Can we do more?
common.qry_engine.execute('ALTER TABLE %s ADD COLUMN %s %s' %
('`' + self.tbl.schema + '`.`' + self.tbl.name + '`',
'`' + self.outputs[new_col] + '`', 'VARCHAR(50)'))
except exc.SQLAlchemyError as msg:
raise GRError(desc='Unable to physically add derived column to table. Contact support.',
data=str(self.outputs), other_info=str(msg))
try: # Refresh the metadata to show the new column
self.tbl = sqlalchemy.Table(self.tbl.name, self.tbl.metadata, extend_existing=True, autoload=True)
except exc.SQLAlchemyError as msg:
raise GRError(desc='Unable to establish metadata for new column. Contact support.',
data=str(self.outputs), other_info=str(msg))

Yes you can
Install sqlalchemy-migrate (pip install sqlalchemy-migrate) and use it in your script to call Table and Column create() method:
from sqlalchemy import String, MetaData, create_engine
from migrate.versioning.schema import Table, Column
db_engine = create_engine(app.config.get('SQLALCHEMY_DATABASE_URI'))
db_meta = MetaData(bind=db_engine)
table = Table('tabel_name' , db_meta)
col = Column('new_column_name', String(20), default='foo')
col.create(table)

Just continuing the simple way proposed by chasmani, little improvement
'''
# simple migration
# columns to add:
# last_status_change = Column(BigInteger, default=None)
# last_complete_phase = Column(String, default=None)
# complete_percentage = Column(DECIMAL, default=0.0)
'''
import sqlite3
from config import APP_STATUS_DB
from sqlalchemy import types
def add_column(database_name: str, table_name: str, column_name: str, data_type: types, default=None):
ret = False
if default is not None:
try:
float(default)
ddl = ("ALTER TABLE '{table_name}' ADD column '{column_name}' '{data_type}' DEFAULT {default}")
except:
ddl = ("ALTER TABLE '{table_name}' ADD column '{column_name}' '{data_type}' DEFAULT '{default}'")
else:
ddl = ("ALTER TABLE '{table_name}' ADD column '{column_name}' '{data_type}'")
sql_command = ddl.format(table_name=table_name, column_name=column_name, data_type=data_type.__name__,
default=default)
try:
connection = sqlite3.connect(database_name)
cursor = connection.cursor()
cursor.execute(sql_command)
connection.commit()
connection.close()
ret = True
except Exception as e:
print(e)
ret = False
return ret
add_column(APP_STATUS_DB, 'procedures', 'last_status_change', types.BigInteger)
add_column(APP_STATUS_DB, 'procedures', 'last_complete_phase', types.String)
add_column(APP_STATUS_DB, 'procedures', 'complete_percentage', types.DECIMAL, 0.0)

If using docker:
go to the terminal of the container holding your DB
get into the db: psql -U usr [YOUR_DB_NAME]
now you can alter tables using raw SQL: alter table [TABLE_NAME] add column [COLUMN_NAME] [TYPE]
Note you will need to have mounted your DB for the changes to persist between builds.

Adding the column "manually" (not using python or SQLAlchemy) is perhaps the easiest?

Same problem over here. What I will do is iterating over the db and add each entry to a new database with the extra column, then delete the old db and rename the new to this one.

Related

SQLAlchemy 1.4 tutorial code "'Connection' object has no attribute 'commit'" error or does not commit changes

Here is some custom code I wrote that I think might be problematic for this particular use case.
class SQLServerConnection:
def __init__(self, database):
...
self.connection_string = \
"DRIVER=" + str(self.driver) + ";" + \
"SERVER=" + str(self.server) + ";" + \
"DATABASE=" + str(self.database) + ";" + \
"Trusted_Connection=yes;"
self.engine = sqlalchemy.create_engine(
sqlalchemy.engine.URL.create(
"mssql+pyodbc", \
query={'odbc_connect': self.connection_string}
)
)
# Runs a command and returns in plain text (python list for multiple rows)
# Can be a select, alter table, anything like that
def execute(self, command, params=False):
# Make a connection object with the server
with self.engine.connect() as conn:
# Can send some parameters along with a plain text query...
# could be single dict or list of dict
# Doc: https://docs.sqlalchemy.org/en/14/tutorial/dbapi_transactions.html#sending-multiple-parameters
if params:
output = conn.execute(sqlalchemy.text(command,params))
else:
output = conn.execute(sqlalchemy.text(command))
# Tell SQL server to save your changes (assuming that is applicable, is not with select)
# Doc: https://docs.sqlalchemy.org/en/14/tutorial/dbapi_transactions.html#committing-changes
try:
conn.commit()
except Exception as e:
#pass
warn("Could not commit changes...\n" + str(e))
# Try to consolidate select statement result into single object to return
try:
output = output.all()
except:
pass
return output
If I try:
cnxn = SQLServerConnection(database='MyDatabase')
cnxn.execute("SELECT * INTO [dbo].[MyTable_newdata] FROM [dbo].[MyTable] ")
or
cnxn.execute("SELECT TOP 0 * INTO [dbo].[MyTable_newdata] FROM [dbo].[MyTable] ")
Python returns this object without error, <sqlalchemy.engine.cursor.LegacyCursorResult at 0x2b793d71880>, but upon looking in MS SQL Server, the new table was not generated. I am not warned about the commit step failing with the SELECT TOP 0 way; I am warned ('Connection' object has no attribute 'commit') in the above way.
CREATE TABLE, ALTER TABLE, or SELECT (etc) appears to work fine, but SELECT * INTO seems to not be working, and I'm not sure how to troubleshoot further. Copy-pasting the query into SQL Server and running appears to work fine.
As noted in the introduction to the 1.4 tutorial here:
A Note on the Future
This tutorial describes a new API that’s released in SQLAlchemy 1.4 known as 2.0 style. The purpose of the 2.0-style API is to provide forwards compatibility with SQLAlchemy 2.0, which is planned as the next generation of SQLAlchemy.
In order to provide the full 2.0 API, a new flag called future will be used, which will be seen as the tutorial describes the Engine and Session objects. These flags fully enable 2.0-compatibility mode and allow the code in the tutorial to proceed fully. When using the future flag with the create_engine() function, the object returned is a subclass of sqlalchemy.engine.Engine described as sqlalchemy.future.Engine. This tutorial will be referring to sqlalchemy.future.Engine.
That is, it is assumed that the engine is created with
engine = create_engine(connection_url, future=True)
You are getting the "'Connection' object has no attribute 'commit'" error because you are creating an old-style Engine object.
You can avoid the error by adding future=True to your create_engine() call:
self.engine = sqlalchemy.create_engine(
sqlalchemy.engine.URL.create(
"mssql+pyodbc",
query={'odbc_connect': self.connection_string}
),
future=True
)
Use this recipe instead:
#!python
from sqlalchemy.sql import Select
from sqlalchemy.ext.compiler import compiles
class SelectInto(Select):
def __init__(self, columns, into, *arg, **kw):
super(SelectInto, self).__init__(columns, *arg, **kw)
self.into = into
#compiles(SelectInto)
def s_into(element, compiler, **kw):
text = compiler.visit_select(element)
text = text.replace('FROM',
'INTO TEMPORARY TABLE %s FROM' %
element.into)
return text
if __name__ == '__main__':
from sqlalchemy.sql import table, column
marker = table('marker',
column('x1'),
column('x2'),
column('x3')
)
print SelectInto([marker.c.x1, marker.c.x2], "tmp_markers").\
where(marker.c.x3==5).\
where(marker.c.x1.in_([1, 5]))
This needs some tweaking, hence it will replace all subquery selects as select INTOs, but test it for now, if it worked it would be better than raw text statments.
Have you tried this from this answer by #Michael Berkowski:
INSERT INTO assets_copy
SELECT * FROM assets;
The answer states that MySQL documentation states that SELECT * INTO isn't supported.

How to extract data from Oracle database with AWS Glue and other AWS services

I am new to AWS glue and other AWS stuff. I have a requirement to build an ETL framework for a project.
This is the high-level diagram. I want to understand, instead of creating 400 glue pipelines, can I create a template kind of a thing which is driven by reference data from a postgres aurora/mysql. I am familiar with Python.
Anyone has any ideas on this? Any references, code examples.
We had a config master table in our mysql db. The columns per convenience we had source_table_name as the identifier to fetch appropriate table column names/queries for CREATING STG TABLE, LOAD DATA INTO STG TABLE, INSERT/UPDATE INTO TARGET TABLEs etc.
We have also split the INSERT/UPDATE into two different columns in config master, since we were using ON DUPLICATE KEY to update existing records.
get the source table name, by processing the lambda events which will have landing file name.
Fetch all required data from the config master for the source table name. It would be something like following:
sql_query = "SELECT * FROM {0}.CONFIG_MASTER WHERE src_tbl_name = %s ".format(mydb)
cur.execute(sql_query, (source_fname))
result = cur.fetchall()
for row in result:
stg_table_name = row[1]
tgt_table_name = row[2]
create_stg_table_qry = row[3]
load_data_stg_table_qry = row[4]
insert_tgt_table_qry = row[5]
insert_tgt_table_qry_part_1 = row[6]
insert_tgt_table_qry_part_2 = row[7]
conn.commit()
cur.close()
Pass appropriate parameters to the generic functions as below:
create_stg_table(stg_table_name, create_stg_table_qry, load_data_stg_table_qry)
loaddata(tgt_table_name, insert_tgt_table_qry_part_1, insert_tgt_table_qry_part_2, stg_table_name)
The generic functions would be something like below, this is for aurora RDS, please make changes as needed.
def create_stg_table(stg_table_name, create_stg_table_qry, load_data_stg_table_qry):
cur, conn = connect()
createStgTable1 = "DROP TABLE IF EXISTS {0}.{1}".format(mydb, stg_table_name)
createStgTable2 = "CREATE TABLE {0}.{1} {2}".format(mydb, stg_table_name, create_stg_table_qry)
loadQry = "LOAD DATA FROM S3 PREFIX 's3://' REPLACE INTO TABLE ...".format()
cur.execute(createStgTable1)
cur.execute(createStgTable2)
cur.execute(loadQry)
conn.commit()
conn.close()
def loaddata(tgt_table_name, insert_tgt_table_qry_part_1, insert_tgt_table_qry_part_2, stg_table_name):
cur, conn = connect()
insertQry = "INSERT INTO target table, from the staging table query here"
print(insertQry)
cur.execute(insertQry)
conn.commit()
conn.close()
Hope this gives an idea.
Thanks

python sqlite - deleting selected records

I'm trying to use sqlite3 in python to delete a selection of rows from a table. My attempt fails, but I can't work out why.
The sql query works ok, but I can't implement it within the python code.
I have a set of records that are moved from current_table to archive_table after a period of time.
I'd like to clean up the current_table by removing those rows that are in the archive_table (matched on id).
Intended SQL query:
DELETE FROM current_table WHERE id IN ( SELECT id FROM archive_table);
Attempted python code:
import sqlite3
def clean_up(current_table, archive_table):
db = sqlite3.connect(sqlite_db)
cursor = db.cursor()
sql_query_delete = '''DELETE FROM %s WHERE id IN ( SELECT id FROM %s);''' % (current_table, archive_table)
try:
cursor.execute(sql_query_delete)
db.commit()
db.close()
except:
print("error deleting")
Now working. The database file was locked by another process. Removing the pointless try/except led me to the detailed error message.

Specifying pyODBC options (fast_executemany = True in particular) using SQLAlchemy

I would like to switch on the fast_executemany option for the pyODBC driver while using SQLAlchemy to insert rows to a table. By default it is of and the code runs really slow... Could anyone suggest how to do this?
Edits:
I am using pyODBC 4.0.21 and SQLAlchemy 1.1.13 and a simplified sample of the code I am using are presented below.
import sqlalchemy as sa
def InsertIntoDB(self, tablename, colnames, data, create = False):
"""
Inserts data into given db table
Args:
tablename - name of db table with dbname
colnames - column names to insert to
data - a list of tuples, a tuple per row
"""
# reflect table into a sqlalchemy object
meta = sa.MetaData(bind=self.engine)
reflected_table = sa.Table(tablename, meta, autoload=True)
# prepare an input object for sa.connection.execute
execute_inp = []
for i in data:
execute_inp.append(dict(zip(colnames, i)))
# Insert values
self.connection.execute(reflected_table.insert(),execute_inp)
Try this for pyodbc
crsr = cnxn.cursor()
crsr.fast_executemany = True
Starting with version 1.3, SQLAlchemy has directly supported fast_executemany, e.g.,
engine = create_engine(connection_uri, fast_executemany=True)

Can't write into mysql database from python

I'm trying to save an object into a mysql table. I created a database with a table, in this table there's a text column.
my actual code is
conn = MySQLdb.connect(host='localhost', user='root', passwd='password',db='database')
x = conn.cursor()
x.execute("""INSERT INTO table (title) VALUES (%s)""", (test,))
where test is the object I created parsing from json. After entering this command python shows 1L but when in sql i do
select * from table;
nothing appears, what is wrong?
You need to commit the changes you make to the data base. Use:
x.execute(...)
conn.commit()
I'd try one of two things. If I have to go with a full script like that, I don't bother using the conn... I'll do a subprocess call.
# farm_out_to_os.py
cmd = """INSERT INTO table (title) VALUES ({})""".format(test))
subprocess.call("mysql -u{} -p{} < {}".format(uname, pwd, cmd), shell=True)
But if you want to do it more programmatically, maybe consider using a full ORM like SQLAlchemy
# models.py
import sqlalchemy as db
from sqlalchemy import declarative_base
Base = declarative_base()
class MyTable(Base):
__tablename__ = 'mytable'
id = db.Column(db.Integer, primary_key=True)
val = db.Column(db.Integer)
def __init__(self, val):
self.val = val
And the code:
# code.py
from sqlalchemy import create_engine, sessionmaker
engine = create_engine(config.SQLALCHEMY_URL)
session = sqlalchemy.sessionmaker(bind=engine)
newval = models.MyTable(val=5)
session.add(newval)
session.commit()
session.close()
Depends on what you're trying to do :)

Categories