refactoring version 2.0
This commit is contained in:
Steve Nyemba
parent
764b3d6af0
commit
e7838f5de1
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@ -48,24 +48,8 @@ import typer
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import os
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import os
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import transport
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import transport
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from transport import etl
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from transport import etl
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from transport import providers
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# from transport import providers
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# SYS_ARGS = {}
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# if len(sys.argv) > 1:
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# N = len(sys.argv)
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# for i in range(1,N):
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# value = None
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# if sys.argv[i].startswith('--'):
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# key = sys.argv[i][2:] #.replace('-','')
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# SYS_ARGS[key] = 1
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# if i + 1 < N:
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# value = sys.argv[i + 1] = sys.argv[i+1].strip()
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# if key and value and not value.startswith('--'):
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# SYS_ARGS[key] = value
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# i += 2
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app = typer.Typer()
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app = typer.Typer()
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@ -77,7 +61,7 @@ def wait(jobs):
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jobs = [thread for thread in jobs if thread.is_alive()]
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jobs = [thread for thread in jobs if thread.is_alive()]
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time.sleep(1)
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time.sleep(1)
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@app.command()
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@app.command(name="apply")
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def move (path,index=None):
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def move (path,index=None):
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_proxy = lambda _object: _object.write(_object.read())
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_proxy = lambda _object: _object.write(_object.read())
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@ -90,27 +74,14 @@ def move (path,index=None):
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etl.instance(**_config)
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etl.instance(**_config)
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else:
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else:
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etl.instance(config=_config)
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etl.instance(config=_config)
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@app.command(name="providers")
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def supported (format:str="table") :
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"""
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This function will print supported providers and their associated classifications
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"""
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_df = (transport.supported())
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print (json.dumps(_df.to_dict(orient="list")))
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#
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# if type(_config) == dict :
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# _object = transport.etl.instance(**_config)
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# _proxy(_object)
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# else:
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# #
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# # here we are dealing with a list of objects (long ass etl job)
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# jobs = []
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# failed = []
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# for _args in _config :
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# if index and _config.index(_args) != index :
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# continue
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# _object=transport.etl.instance(**_args)
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# thread = Process(target=_proxy,args=(_object,))
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# thread.start()
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# jobs.append(thread())
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# if _config.index(_args) == 0 :
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# thread.join()
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# wait(jobs)
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@app.command()
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@app.command()
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def version():
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def version():
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print (transport.version.__version__)
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print (transport.version.__version__)
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@ -1,5 +1,5 @@
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__author__ = 'The Phi Technology'
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__author__ = 'The Phi Technology'
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__version__= '1.9.8.20'
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__version__= '2.0.0'
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__license__="""
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__license__="""
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@ -11,360 +11,79 @@ This library is designed to serve as a wrapper to a set of supported data stores
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- s3
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- s3
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- sqlite
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- sqlite
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The supported operations are read/write and providing meta data to the calling code
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The supported operations are read/write and providing meta data to the calling code
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Requirements :
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We separated reads from writes to mitigate accidents associated with writes.
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pymongo
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Source Code is available under MIT License:
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boto
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https://healthcareio.the-phi.com/data-transport
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couldant
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https://hiplab.mc.vanderbilt.edu/git/hiplab/data-transport
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The configuration for the data-store is as follows :
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e.g:
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mongodb
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provider:'mongodb',[port:27017],[host:localhost],db:<name>,doc:<_name>,context:<read|write>
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"""
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"""
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# import pandas as pd
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# import numpy as np
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import json
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import importlib
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import sys
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import sqlalchemy
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from datetime import datetime
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if sys.version_info[0] > 2 :
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# from transport.common import Reader, Writer,Console #, factory
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from transport import disk
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from transport import s3 as s3
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from transport import rabbitmq as queue
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from transport import couch as couch
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from transport import mongo as mongo
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from transport import sql as sql
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from transport import etl as etl
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# from transport.version import __version__
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from info import __version__,__author__
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from transport import providers
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else:
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from common import Reader, Writer,Console #, factory
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import disk
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import queue
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import couch
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import mongo
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import s3
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import sql
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import etl
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from info import __version__,__author__
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import providers
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import numpy as np
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import numpy as np
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from psycopg2.extensions import register_adapter, AsIs
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from transport import sql, nosql, cloud, other
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register_adapter(np.int64, AsIs)
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import pandas as pd
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import json
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# import psycopg2 as pg
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# import mysql.connector as my
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# from google.cloud import bigquery as bq
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# import nzpy as nz #--- netezza drivers
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import os
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import os
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from info import __version__,__author__
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# class providers :
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PROVIDERS = {}
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# POSTGRESQL = 'postgresql'
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def init():
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# MONGODB = 'mongodb'
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global PROVIDERS
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for _module in [cloud,sql,nosql,other] :
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# BIGQUERY ='bigquery'
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for _provider_name in dir(_module) :
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# FILE = 'file'
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if _provider_name.startswith('__') :
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# ETL = 'etl'
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continue
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# SQLITE = 'sqlite'
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PROVIDERS[_provider_name] = {'module':getattr(_module,_provider_name),'type':_module.__name__}
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# SQLITE3= 'sqlite'
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# print ([ {name:getattr(sql,name)} for name in dir(sql) if not name.startswith('__')])
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# REDSHIFT = 'redshift'
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# NETEZZA = 'netezza'
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# MYSQL = 'mysql'
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# RABBITMQ = 'rabbitmq'
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# MARIADB = 'mariadb'
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# COUCHDB = 'couch'
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# CONSOLE = 'console'
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# ETL = 'etl'
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# #
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# # synonyms of the above
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# BQ = BIGQUERY
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# MONGO = MONGODB
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# FERRETDB= MONGODB
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# PG = POSTGRESQL
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# PSQL = POSTGRESQL
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# PGSQL = POSTGRESQL
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# import providers
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# class IEncoder (json.JSONEncoder):
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# def IEncoder (self,object):
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# if type(object) == np.integer :
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# return int(object)
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# elif type(object) == np.floating:
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# return float(object)
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# elif type(object) == np.ndarray :
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# return object.tolist()
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# elif type(object) == datetime :
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# return o.isoformat()
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# else:
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# return super(IEncoder,self).default(object)
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def instance (**_args):
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"""
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type:
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read: true|false (default true)
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auth_file
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"""
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global PROVIDERS
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if 'auth_file' in _args:
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if os.path.exists(_args['auth_file']) :
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f = open(_args['auth_file'])
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_args = dict (_args,** json.loads(f.read()) )
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f.close()
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else:
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filename = _args['auth_file']
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raise Exception(f" {filename} was not found or is invalid")
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if _args['provider'] in PROVIDERS :
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_info = PROVIDERS[_args['provider']]
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_module = _info['module']
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if 'context' in _args :
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_context = _args['context']
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else:
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_context = 'read'
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_pointer = getattr(_module,'Reader') if _context == 'read' else getattr(_module,'Writer')
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return _pointer (**_args)
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pass
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else:
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raise Exception ("Missing or Unknown provider")
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pass
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def supported ():
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_info = {}
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for _provider in PROVIDERS :
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_item = PROVIDERS[_provider]
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if _item['type'] not in _info :
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_info[_item['type']] = []
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_info[_item['type']].append(_provider)
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_df = pd.DataFrame()
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for _id in _info :
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if not _df.shape[0] :
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_df = pd.DataFrame(_info[_id],columns=[_id.replace('transport.','')])
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else:
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_df = pd.DataFrame(_info[_id],columns=[_id.replace('transport.','')]).join(_df, how='outer')
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return _df.fillna('')
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class factory :
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class factory :
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# TYPE = {"sql":{"providers":["postgresql","mysql","neteeza","bigquery","mariadb","redshift"]}}
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pass
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# PROVIDERS = {
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factory.instance = instance
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# "etl":{"class":{"read":etl.instance,"write":etl.instance}},
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init()
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# # "console":{"class":{"write":Console,"read":Console}},
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# if __name__ == '__main__' :
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# "file":{"class":{"read":disk.DiskReader,"write":disk.DiskWriter}},
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# # if not PROVIDERS :
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# "sqlite":{"class":{"read":disk.SQLiteReader,"write":disk.SQLiteWriter}},
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# init()
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# "postgresql":{"port":5432,"host":"localhost","database":None,"driver":pg,"default":{"type":"VARCHAR"},"class":{"read":sql.SQLReader,"write":sql.SQLWriter}},
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# print (list(PROVIDERS.keys()))
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# "redshift":{"port":5432,"host":"localhost","database":None,"driver":pg,"default":{"type":"VARCHAR"},"class":{"read":sql.SQLReader,"write":sql.SQLWriter}},
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# pgr = instance(provider='postgresql',database='io',table='foo',write=True)
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# "bigquery":{"class":{"read":sql.BQReader,"write":sql.BQWriter}},
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# print (pgr.read())
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# "mysql":{"port":3306,"host":"localhost","default":{"type":"VARCHAR(256)"},"driver":my,"class":{"read":sql.SQLReader,"write":sql.SQLWriter}},
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# print ()
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# "mariadb":{"port":3306,"host":"localhost","default":{"type":"VARCHAR(256)"},"driver":my,"class":{"read":sql.SQLReader,"write":sql.SQLWriter}},
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# print (supported())
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# "mongo":{"port":27017,"host":"localhost","class":{"read":mongo.MongoReader,"write":mongo.MongoWriter}},
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# "couch":{"port":5984,"host":"localhost","class":{"read":couch.CouchReader,"write":couch.CouchWriter}},
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# "netezza":{"port":5480,"driver":nz,"default":{"type":"VARCHAR(256)"},"class":{"read":sql.SQLReader,"write":sql.SQLWriter}},
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# "rabbitmq":{"port":5672,"host":"localhost","class":{"read":queue.QueueReader,"write":queue.QueueWriter,"listen":queue.QueueListener,"listener":queue.QueueListener},"default":{"type":"application/json"}}}
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# #
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# # creating synonyms
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# PROVIDERS['mongodb'] = PROVIDERS['mongo']
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# PROVIDERS['couchdb'] = PROVIDERS['couch']
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# PROVIDERS['bq'] = PROVIDERS['bigquery']
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# PROVIDERS['sqlite3'] = PROVIDERS['sqlite']
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# PROVIDERS['rabbit'] = PROVIDERS['rabbitmq']
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# PROVIDERS['rabbitmq-server'] = PROVIDERS['rabbitmq']
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@staticmethod
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def instance(**_args):
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if 'type' in _args :
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#
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# Legacy code being returned
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return factory._instance(**_args);
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else:
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return instance(**_args)
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@staticmethod
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def _instance(**args):
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"""
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This class will create an instance of a transport when providing
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:type name of the type we are trying to create
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:args The arguments needed to create the instance
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"""
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source = args['type']
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params = args['args']
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anObject = None
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if source in ['HttpRequestReader','HttpSessionWriter']:
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#
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# @TODO: Make sure objects are serializable, be smart about them !!
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#
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aClassName = ''.join([source,'(**params)'])
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else:
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stream = json.dumps(params)
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aClassName = ''.join([source,'(**',stream,')'])
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try:
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anObject = eval( aClassName)
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#setattr(anObject,'name',source)
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except Exception as e:
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print(['Error ',e])
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return anObject
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import time
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def instance(**_pargs):
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"""
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creating an instance given the provider, we should have an idea of :class, :driver
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:provider
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:read|write = {connection to the database}
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"""
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#
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# @TODO: provide authentication file that will hold all the parameters, that will later on be used
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#
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_args = dict(_pargs,**{})
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if 'auth_file' in _args :
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path = _args['auth_file']
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file = open(path)
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_config = json.loads( file.read())
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_args = dict(_args,**_config)
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file.close()
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_provider = _args['provider']
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_context = list( set(['read','write','listen']) & set(_args.keys()) )
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if _context :
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_context = _context[0]
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else:
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_context = _args['context'] if 'context' in _args else 'read'
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# _group = None
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# for _id in providers.CATEGORIES :
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# if _provider in providers.CATEGORIES[_id] :
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# _group = _id
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# break
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# if _group :
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if _provider in providers.PROVIDERS and _context in providers.PROVIDERS[_provider]:
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# _classPointer = _getClassInstance(_group,**_args)
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_classPointer = providers.PROVIDERS[_provider][_context]
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#
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# Let us reformat the arguments
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# if 'read' in _args or 'write' in _args :
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# _args = _args['read'] if 'read' in _args else _args['write']
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# _args['provider'] = _provider
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# if _group == 'sql' :
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if _provider in providers.CATEGORIES['sql'] :
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_info = _get_alchemyEngine(**_args)
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_args = dict(_args,**_info)
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_args['driver'] = providers.DRIVERS[_provider]
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else:
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if _provider in providers.DEFAULT :
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_default = providers.DEFAULT[_provider]
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_defkeys = list(set(_default.keys()) - set(_args.keys()))
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if _defkeys :
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for key in _defkeys :
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_args[key] = _default[key]
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pass
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#
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# get default values from
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return _classPointer(**_args)
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#
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# Let us determine the category of the provider that has been given
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def _get_alchemyEngine(**_args):
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"""
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This function returns the SQLAlchemy engine associated with parameters, This is only applicable for SQL _items
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:_args arguments passed to the factory {provider and other}
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"""
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_provider = _args['provider']
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_pargs = {}
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if _provider == providers.SQLITE3 :
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_path = _args['database'] if 'database' in _args else _args['path']
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uri = ''.join([_provider,':///',_path])
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else:
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#@TODO: Enable authentication files (private_key)
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_username = _args['username'] if 'username' in _args else ''
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_password = _args['password'] if 'password' in _args else ''
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|
||||||
_account = _args['account'] if 'account' in _args else ''
|
|
||||||
_database = _args['database'] if 'database' in _args else _args['path']
|
|
||||||
|
|
||||||
if _username != '':
|
|
||||||
_account = _username + ':'+_password+'@'
|
|
||||||
_host = _args['host'] if 'host' in _args else ''
|
|
||||||
_port = _args['port'] if 'port' in _args else ''
|
|
||||||
if _provider in providers.DEFAULT :
|
|
||||||
_default = providers.DEFAULT[_provider]
|
|
||||||
_host = _host if _host != '' else (_default['host'] if 'host' in _default else '')
|
|
||||||
_port = _port if _port != '' else (_default['port'] if 'port' in _default else '')
|
|
||||||
if _port == '':
|
|
||||||
_port = providers.DEFAULT['port'] if 'port' in providers.DEFAULT else ''
|
|
||||||
#
|
|
||||||
|
|
||||||
if _host != '' and _port != '' :
|
|
||||||
_fhost = _host+":"+str(_port) #--formatted hostname
|
|
||||||
else:
|
|
||||||
_fhost = _host
|
|
||||||
# Let us update the parameters we have thus far
|
|
||||||
#
|
|
||||||
|
|
||||||
|
|
||||||
uri = ''.join([_provider,"://",_account,_fhost,'/',_database])
|
|
||||||
_pargs = {'host':_host,'port':_port,'username':_username,'password':_password}
|
|
||||||
_engine = sqlalchemy.create_engine (uri,future=True)
|
|
||||||
_out = {'sqlalchemy':_engine}
|
|
||||||
|
|
||||||
for key in _pargs :
|
|
||||||
if _pargs[key] != '' :
|
|
||||||
_out[key] = _pargs[key]
|
|
||||||
return _out
|
|
||||||
@DeprecationWarning
|
|
||||||
def _getClassInstance(_group,**_args):
|
|
||||||
"""
|
|
||||||
This function returns the class instance we are attempting to instanciate
|
|
||||||
:_group items in providers.CATEGORIES.keys()
|
|
||||||
:_args arguments passed to the factory class
|
|
||||||
"""
|
|
||||||
# if 'read' in _args or 'write' in _args :
|
|
||||||
# _context = 'read' if 'read' in _args else _args['write']
|
|
||||||
# _info = _args[_context]
|
|
||||||
# else:
|
|
||||||
# _context = _args['context'] if 'context' in _args else 'read'
|
|
||||||
# _class = providers.READ[_group] if _context == 'read' else providers.WRITE[_group]
|
|
||||||
# if type(_class) == dict and _args['provider'] in _class:
|
|
||||||
# _class = _class[_args['provider']]
|
|
||||||
|
|
||||||
# return _class
|
|
||||||
|
|
||||||
@DeprecationWarning
|
|
||||||
def __instance(**_args):
|
|
||||||
"""
|
|
||||||
|
|
||||||
@param provider {file,sqlite,postgresql,redshift,bigquery,netezza,mongo,couch ...}
|
|
||||||
@param context read|write|rw
|
|
||||||
@param _args argument to got with the datastore (username,password,host,port ...)
|
|
||||||
"""
|
|
||||||
|
|
||||||
provider = _args['provider']
|
|
||||||
context = _args['context']if 'context' in _args else None
|
|
||||||
_id = context if context in list(factory.PROVIDERS[provider]['class'].keys()) else 'read'
|
|
||||||
if _id :
|
|
||||||
args = {'provider':_id}
|
|
||||||
for key in factory.PROVIDERS[provider] :
|
|
||||||
if key == 'class' :
|
|
||||||
continue
|
|
||||||
value = factory.PROVIDERS[provider][key]
|
|
||||||
args[key] = value
|
|
||||||
#
|
|
||||||
#
|
|
||||||
|
|
||||||
args = dict(args,**_args)
|
|
||||||
|
|
||||||
# print (provider in factory.PROVIDERS)
|
|
||||||
if 'class' in factory.PROVIDERS[provider]:
|
|
||||||
pointer = factory.PROVIDERS[provider]['class'][_id]
|
|
||||||
else:
|
|
||||||
pointer = sql.SQLReader if _id == 'read' else sql.SQLWriter
|
|
||||||
#
|
|
||||||
# Let us try to establish an sqlalchemy wrapper
|
|
||||||
try:
|
|
||||||
account = ''
|
|
||||||
host = ''
|
|
||||||
if provider not in [providers.BIGQUERY,providers.MONGODB, providers.COUCHDB, providers.SQLITE, providers.CONSOLE,providers.ETL, providers.FILE, providers.RABBITMQ] :
|
|
||||||
# if provider not in ['bigquery','mongodb','mongo','couchdb','sqlite','console','etl','file','rabbitmq'] :
|
|
||||||
#
|
|
||||||
# In these cases we are assuming RDBMS and thus would exclude NoSQL and BigQuery
|
|
||||||
username = args['username'] if 'username' in args else ''
|
|
||||||
password = args['password'] if 'password' in args else ''
|
|
||||||
if username == '' :
|
|
||||||
account = ''
|
|
||||||
else:
|
|
||||||
account = username + ':'+password+'@'
|
|
||||||
host = args['host']
|
|
||||||
if 'port' in args :
|
|
||||||
host = host+":"+str(args['port'])
|
|
||||||
|
|
||||||
database = args['database']
|
|
||||||
elif provider in [providers.SQLITE,providers.FILE]:
|
|
||||||
account = ''
|
|
||||||
host = ''
|
|
||||||
database = args['path'] if 'path' in args else args['database']
|
|
||||||
|
|
||||||
if provider not in [providers.MONGODB, providers.COUCHDB, providers.BIGQUERY, providers.CONSOLE, providers.ETL,providers.FILE,providers.RABBITMQ] :
|
|
||||||
# if provider not in ['mongodb','mongo','couchdb','bigquery','console','etl','file','rabbitmq'] :
|
|
||||||
uri = ''.join([provider,"://",account,host,'/',database])
|
|
||||||
|
|
||||||
e = sqlalchemy.create_engine (uri,future=True)
|
|
||||||
args['sqlalchemy'] = e
|
|
||||||
|
|
||||||
#
|
|
||||||
# @TODO: Include handling of bigquery with SQLAlchemy
|
|
||||||
except Exception as e:
|
|
||||||
print (_args)
|
|
||||||
print (e)
|
|
||||||
|
|
||||||
return pointer(**args)
|
|
||||||
|
|
||||||
return None
|
|
||||||
|
|
@ -0,0 +1,6 @@
|
||||||
|
"""
|
||||||
|
Steve L. Nyemba, nyemba@gmail.com
|
||||||
|
This namespace implements support for cloud databases databricks,bigquery ...
|
||||||
|
"""
|
||||||
|
from . import bigquery, databricks, nextcloud, s3
|
||||||
|
|
||||||
|
|
@ -0,0 +1,156 @@
|
||||||
|
"""
|
||||||
|
Implementing support for google's bigquery
|
||||||
|
- cloud.bigquery.Read
|
||||||
|
- cloud.bigquery.Write
|
||||||
|
"""
|
||||||
|
import json
|
||||||
|
from google.oauth2 import service_account
|
||||||
|
from google.cloud import bigquery as bq
|
||||||
|
|
||||||
|
from multiprocessing import Lock, RLock
|
||||||
|
import pandas as pd
|
||||||
|
import pandas_gbq as pd_gbq
|
||||||
|
import numpy as np
|
||||||
|
import time
|
||||||
|
|
||||||
|
MAX_CHUNK = 2000000
|
||||||
|
class BigQuery:
|
||||||
|
def __init__(self,**_args):
|
||||||
|
path = _args['service_key'] if 'service_key' in _args else _args['private_key']
|
||||||
|
self.credentials = service_account.Credentials.from_service_account_file(path)
|
||||||
|
self.dataset = _args['dataset'] if 'dataset' in _args else None
|
||||||
|
self.path = path
|
||||||
|
self.dtypes = _args['dtypes'] if 'dtypes' in _args else None
|
||||||
|
self.table = _args['table'] if 'table' in _args else None
|
||||||
|
self.client = bq.Client.from_service_account_json(self.path)
|
||||||
|
def meta(self,**_args):
|
||||||
|
"""
|
||||||
|
This function returns meta data for a given table or query with dataset/table properly formatted
|
||||||
|
:param table name of the name WITHOUT including dataset
|
||||||
|
:param sql sql query to be pulled,
|
||||||
|
"""
|
||||||
|
table = _args['table'] if 'table' in _args else self.table
|
||||||
|
|
||||||
|
try:
|
||||||
|
if table :
|
||||||
|
_dataset = self.dataset if 'dataset' not in _args else _args['dataset']
|
||||||
|
sql = f"""SELECT column_name as name, data_type as type FROM {_dataset}.INFORMATION_SCHEMA.COLUMNS WHERE table_name = '{table}' """
|
||||||
|
_info = {'credentials':self.credentials,'dialect':'standard'}
|
||||||
|
return pd_gbq.read_gbq(sql,**_info).to_dict(orient='records')
|
||||||
|
# return self.read(sql=sql).to_dict(orient='records')
|
||||||
|
# ref = self.client.dataset(self.dataset).table(table)
|
||||||
|
|
||||||
|
# _schema = self.client.get_table(ref).schema
|
||||||
|
# return [{"name":_item.name,"type":_item.field_type,"description":( "" if not hasattr(_item,"description") else _item.description )} for _item in _schema]
|
||||||
|
else :
|
||||||
|
return []
|
||||||
|
except Exception as e:
|
||||||
|
|
||||||
|
return []
|
||||||
|
def has(self,**_args):
|
||||||
|
found = False
|
||||||
|
try:
|
||||||
|
_has = self.meta(**_args)
|
||||||
|
found = _has is not None and len(_has) > 0
|
||||||
|
except Exception as e:
|
||||||
|
pass
|
||||||
|
return found
|
||||||
|
class Reader (BigQuery):
|
||||||
|
"""
|
||||||
|
Implementing support for reading from bigquery, This class acts as a wrapper around google's API
|
||||||
|
"""
|
||||||
|
def __init__(self,**_args):
|
||||||
|
|
||||||
|
super().__init__(**_args)
|
||||||
|
def apply(self,sql):
|
||||||
|
return self.read(sql=sql)
|
||||||
|
|
||||||
|
def read(self,**_args):
|
||||||
|
SQL = None
|
||||||
|
table = self.table if 'table' not in _args else _args['table']
|
||||||
|
if 'sql' in _args :
|
||||||
|
SQL = _args['sql']
|
||||||
|
elif table:
|
||||||
|
|
||||||
|
table = "".join(["`",table,"`"]) if '.' in table else "".join(["`:dataset.",table,"`"])
|
||||||
|
SQL = "SELECT * FROM :table ".replace(":table",table)
|
||||||
|
if not SQL :
|
||||||
|
return None
|
||||||
|
if SQL and 'limit' in _args:
|
||||||
|
SQL += " LIMIT "+str(_args['limit'])
|
||||||
|
if (':dataset' in SQL or ':DATASET' in SQL) and self.dataset:
|
||||||
|
SQL = SQL.replace(':dataset',self.dataset).replace(':DATASET',self.dataset)
|
||||||
|
_info = {'credentials':self.credentials,'dialect':'standard'}
|
||||||
|
return pd_gbq.read_gbq(SQL,**_info) if SQL else None
|
||||||
|
# return self.client.query(SQL).to_dataframe() if SQL else None
|
||||||
|
|
||||||
|
class Writer (BigQuery):
|
||||||
|
"""
|
||||||
|
This class implements support for writing against bigquery
|
||||||
|
"""
|
||||||
|
lock = RLock()
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
|
||||||
|
self.parallel = False if 'lock' not in _args else _args['lock']
|
||||||
|
self.table = _args['table'] if 'table' in _args else None
|
||||||
|
self.mode = {'if_exists':'append','chunksize':900000,'destination_table':self.table,'credentials':self.credentials}
|
||||||
|
self._chunks = 1 if 'chunks' not in _args else int(_args['chunks'])
|
||||||
|
self._location = 'US' if 'location' not in _args else _args['location']
|
||||||
|
def write(self,_data,**_args) :
|
||||||
|
"""
|
||||||
|
This function will perform a write to bigquery
|
||||||
|
:_data data-frame to be written to bigquery
|
||||||
|
"""
|
||||||
|
try:
|
||||||
|
if self.parallel or 'lock' in _args :
|
||||||
|
Write.lock.acquire()
|
||||||
|
_args['table'] = self.table if 'table' not in _args else _args['table']
|
||||||
|
self._write(_data,**_args)
|
||||||
|
finally:
|
||||||
|
if self.parallel:
|
||||||
|
Write.lock.release()
|
||||||
|
def submit(self,_sql):
|
||||||
|
"""
|
||||||
|
Write the output of a massive query to a given table, biquery will handle this as a job
|
||||||
|
This function will return the job identifier
|
||||||
|
"""
|
||||||
|
_config = bq.QueryJobConfig()
|
||||||
|
_config.destination = self.client.dataset(self.dataset).table(self.table)
|
||||||
|
_config.allow_large_results = True
|
||||||
|
# _config.write_disposition = bq.bq_consts.WRITE_APPEND
|
||||||
|
_config.dry_run = False
|
||||||
|
# _config.priority = 'BATCH'
|
||||||
|
_resp = self.client.query(_sql,location=self._location,job_config=_config)
|
||||||
|
return _resp.job_id
|
||||||
|
def status (self,_id):
|
||||||
|
return self.client.get_job(_id,location=self._location)
|
||||||
|
def _write(self,_info,**_args) :
|
||||||
|
_df = None
|
||||||
|
if type(_info) in [list,pd.DataFrame] :
|
||||||
|
if type(_info) == list :
|
||||||
|
_df = pd.DataFrame(_info)
|
||||||
|
elif type(_info) == pd.DataFrame :
|
||||||
|
_df = _info
|
||||||
|
|
||||||
|
if '.' not in _args['table'] :
|
||||||
|
self.mode['destination_table'] = '.'.join([self.dataset,_args['table']])
|
||||||
|
else:
|
||||||
|
|
||||||
|
self.mode['destination_table'] = _args['table'].strip()
|
||||||
|
if 'schema' in _args :
|
||||||
|
self.mode['table_schema'] = _args['schema']
|
||||||
|
#
|
||||||
|
# Let us insure that the types are somewhat compatible ...
|
||||||
|
# _map = {'INTEGER':np.int64,'DATETIME':'datetime64[ns]','TIMESTAMP':'datetime64[ns]','FLOAT':np.float64,'DOUBLE':np.float64,'STRING':str}
|
||||||
|
# _mode = copy.deepcopy(self.mode)
|
||||||
|
_mode = self.mode
|
||||||
|
# _df.to_gbq(**self.mode) #if_exists='append',destination_table=partial,credentials=credentials,chunksize=90000)
|
||||||
|
#
|
||||||
|
# Let us adjust the chunking here
|
||||||
|
self._chunks = 10 if _df.shape[0] > MAX_CHUNK and self._chunks == 1 else self._chunks
|
||||||
|
_indexes = np.array_split(np.arange(_df.shape[0]),self._chunks)
|
||||||
|
for i in _indexes :
|
||||||
|
_df.iloc[i].to_gbq(**self.mode)
|
||||||
|
time.sleep(1)
|
||||||
|
pass
|
||||||
|
|
@ -0,0 +1,111 @@
|
||||||
|
"""
|
||||||
|
This file implements databricks handling, This functionality will rely on databricks-sql-connector
|
||||||
|
LICENSE (MIT)
|
||||||
|
Copyright 2016-2020, The Phi Technology LLC
|
||||||
|
|
||||||
|
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
|
||||||
|
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
|
||||||
|
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
||||||
|
|
||||||
|
|
||||||
|
@TODO:
|
||||||
|
- Migrate SQLite to SQL hierarchy
|
||||||
|
- Include Write in Chunks from pandas
|
||||||
|
"""
|
||||||
|
import os
|
||||||
|
import sqlalchemy
|
||||||
|
# from transport.common import Reader,Writer
|
||||||
|
import pandas as pd
|
||||||
|
|
||||||
|
|
||||||
|
class Bricks:
|
||||||
|
"""
|
||||||
|
:host
|
||||||
|
:token
|
||||||
|
:database
|
||||||
|
:cluster_path
|
||||||
|
:table
|
||||||
|
"""
|
||||||
|
def __init__(self,**_args):
|
||||||
|
_host = _args['host']
|
||||||
|
_token= _args['token']
|
||||||
|
_cluster_path = _args['cluster_path']
|
||||||
|
self._schema = _args['schema'] if 'schema' in _args else _args['database']
|
||||||
|
_catalog = _args['catalog']
|
||||||
|
self._table = _args['table'] if 'table' in _args else None
|
||||||
|
|
||||||
|
#
|
||||||
|
# @TODO:
|
||||||
|
# Sometimes when the cluster isn't up and running it takes a while, the user should be alerted of this
|
||||||
|
#
|
||||||
|
|
||||||
|
_uri = f'''databricks+connector://token:{_token}@{_host}?http_path={_cluster_path}&catalog={_catalog}&schema={self._schema}'''
|
||||||
|
self._engine = sqlalchemy.create_engine (_uri)
|
||||||
|
pass
|
||||||
|
def meta(self,**_args):
|
||||||
|
table = _args['table'] if 'table' in _args else self._table
|
||||||
|
if not table :
|
||||||
|
return []
|
||||||
|
else:
|
||||||
|
if sqlalchemy.__version__.startswith('1.') :
|
||||||
|
_m = sqlalchemy.MetaData(bind=self._engine)
|
||||||
|
_m.reflect(only=[table])
|
||||||
|
else:
|
||||||
|
_m = sqlalchemy.MetaData()
|
||||||
|
_m.reflect(bind=self._engine)
|
||||||
|
#
|
||||||
|
# Let's retrieve te information associated with a table
|
||||||
|
#
|
||||||
|
return [{'name':_attr.name,'type':_attr.type} for _attr in _m.tables[table].columns]
|
||||||
|
|
||||||
|
def has(self,**_args):
|
||||||
|
return self.meta(**_args)
|
||||||
|
def apply(self,_sql):
|
||||||
|
try:
|
||||||
|
if _sql.lower().startswith('select') :
|
||||||
|
return pd.read_sql(_sql,self._engine)
|
||||||
|
except Exception as e:
|
||||||
|
pass
|
||||||
|
|
||||||
|
class Reader(Bricks):
|
||||||
|
"""
|
||||||
|
This class is designed for reads and will execute reads against a table name or a select SQL statement
|
||||||
|
"""
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
def read(self,**_args):
|
||||||
|
limit = None if 'limit' not in _args else str(_args['limit'])
|
||||||
|
|
||||||
|
if 'sql' in _args :
|
||||||
|
sql = _args['sql']
|
||||||
|
elif 'table' in _args :
|
||||||
|
table = _args['table']
|
||||||
|
sql = f'SELECT * FROM {table}'
|
||||||
|
if limit :
|
||||||
|
sql = sql + f' LIMIT {limit}'
|
||||||
|
|
||||||
|
if 'sql' in _args or 'table' in _args :
|
||||||
|
return self.apply(sql)
|
||||||
|
else:
|
||||||
|
return pd.DataFrame()
|
||||||
|
pass
|
||||||
|
class Writer(Bricks):
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
def write(self,_data,**_args):
|
||||||
|
"""
|
||||||
|
This data will write data to data-bricks against a given table. If the table is not specified upon initiazation, it can be specified here
|
||||||
|
_data: data frame to push to databricks
|
||||||
|
_args: chunks, table, schema
|
||||||
|
"""
|
||||||
|
_schema = self._schema if 'schema' not in _args else _args['schema']
|
||||||
|
_table = self._table if 'table' not in _args else _args['table']
|
||||||
|
_df = _data if type(_data) == pd.DataFrame else _data
|
||||||
|
if type(_df) == dict :
|
||||||
|
_df = [_df]
|
||||||
|
if type(_df) == list :
|
||||||
|
_df = pd.DataFrame(_df)
|
||||||
|
_df.to_sql(
|
||||||
|
name=_table,schema=_schema,
|
||||||
|
con=self._engine,if_exists='append',index=False);
|
||||||
|
pass
|
||||||
|
|
@ -0,0 +1,80 @@
|
||||||
|
"""
|
||||||
|
We are implementing transport to and from nextcloud (just like s3)
|
||||||
|
"""
|
||||||
|
import os
|
||||||
|
import sys
|
||||||
|
from transport.common import IEncoder
|
||||||
|
import pandas as pd
|
||||||
|
from io import StringIO
|
||||||
|
import json
|
||||||
|
import nextcloud_client as nextcloud
|
||||||
|
|
||||||
|
class Nextcloud :
|
||||||
|
def __init__(self,**_args):
|
||||||
|
pass
|
||||||
|
self._delimiter = None
|
||||||
|
self._handler = nextcloud.Client(_args['url'])
|
||||||
|
_uid = _args['uid']
|
||||||
|
_token = _args['token']
|
||||||
|
self._uri = _args['folder'] if 'folder' in _args else './'
|
||||||
|
if self._uri.endswith('/') :
|
||||||
|
self._uri = self._uri[:-1]
|
||||||
|
self._file = None if 'file' not in _args else _args['file']
|
||||||
|
self._handler.login(_uid,_token)
|
||||||
|
def close(self):
|
||||||
|
try:
|
||||||
|
self._handler.logout()
|
||||||
|
except Exception as e:
|
||||||
|
pass
|
||||||
|
|
||||||
|
|
||||||
|
class Reader(Nextcloud):
|
||||||
|
def __init__(self,**_args):
|
||||||
|
# self._file = [] if 'file' not in _args else _args['file']
|
||||||
|
super().__init__(**_args)
|
||||||
|
pass
|
||||||
|
def read(self,**_args):
|
||||||
|
_filename = self._file if 'file' not in _args else _args['file']
|
||||||
|
#
|
||||||
|
# @TODO: if _filename is none, an exception should be raised
|
||||||
|
#
|
||||||
|
_uri = '/'.join([self._uri,_filename])
|
||||||
|
if self._handler.get_file(_uri) :
|
||||||
|
#
|
||||||
|
#
|
||||||
|
_info = self._handler.file_info(_uri)
|
||||||
|
_content = self._handler.get_file_contents(_uri).decode('utf8')
|
||||||
|
if _info.get_content_type() == 'text/csv' :
|
||||||
|
#
|
||||||
|
# @TODO: enable handling of csv, xls, parquet, pickles
|
||||||
|
_file = StringIO(_content)
|
||||||
|
return pd.read_csv(_file)
|
||||||
|
else:
|
||||||
|
#
|
||||||
|
# if it is neither a structured document like csv, we will return the content as is
|
||||||
|
return _content
|
||||||
|
return None
|
||||||
|
class Writer (Nextcloud):
|
||||||
|
"""
|
||||||
|
This class will write data to an instance of nextcloud
|
||||||
|
"""
|
||||||
|
def __init__(self,**_args) :
|
||||||
|
super().__init__(**_args)
|
||||||
|
self
|
||||||
|
def write(self,_data,**_args):
|
||||||
|
"""
|
||||||
|
This function will upload a file to a given destination
|
||||||
|
:file has the uri of the location of the file
|
||||||
|
"""
|
||||||
|
_filename = self._file if 'file' not in _args else _args['file']
|
||||||
|
_uri = '/'.join([self._uri,_filename])
|
||||||
|
if type(_data) == pd.DataFrame :
|
||||||
|
f = StringIO()
|
||||||
|
_data.to_csv(f,index=False)
|
||||||
|
_content = f.getvalue()
|
||||||
|
elif type(_data) == dict :
|
||||||
|
_content = json.dumps(_data,cls=IEncoder)
|
||||||
|
else:
|
||||||
|
_content = str(_data)
|
||||||
|
self._handler.put_file_contents(_uri,_content)
|
||||||
|
|
||||||
|
|
@ -0,0 +1,127 @@
|
||||||
|
"""
|
||||||
|
Data Transport - 1.0
|
||||||
|
Steve L. Nyemba, The Phi Technology LLC
|
||||||
|
|
||||||
|
This file is a wrapper around s3 bucket provided by AWS for reading and writing content
|
||||||
|
"""
|
||||||
|
from datetime import datetime
|
||||||
|
import boto
|
||||||
|
from boto.s3.connection import S3Connection, OrdinaryCallingFormat
|
||||||
|
import numpy as np
|
||||||
|
import botocore
|
||||||
|
from smart_open import smart_open
|
||||||
|
import sys
|
||||||
|
|
||||||
|
import json
|
||||||
|
from io import StringIO
|
||||||
|
import json
|
||||||
|
|
||||||
|
class s3 :
|
||||||
|
"""
|
||||||
|
@TODO: Implement a search function for a file given a bucket??
|
||||||
|
"""
|
||||||
|
def __init__(self,**args) :
|
||||||
|
"""
|
||||||
|
This function will extract a file or set of files from s3 bucket provided
|
||||||
|
@param access_key
|
||||||
|
@param secret_key
|
||||||
|
@param path location of the file
|
||||||
|
@param filter filename or filtering elements
|
||||||
|
"""
|
||||||
|
try:
|
||||||
|
self.s3 = S3Connection(args['access_key'],args['secret_key'],calling_format=OrdinaryCallingFormat())
|
||||||
|
self.bucket = self.s3.get_bucket(args['bucket'].strip(),validate=False) if 'bucket' in args else None
|
||||||
|
# self.path = args['path']
|
||||||
|
self.filter = args['filter'] if 'filter' in args else None
|
||||||
|
self.filename = args['file'] if 'file' in args else None
|
||||||
|
self.bucket_name = args['bucket'] if 'bucket' in args else None
|
||||||
|
|
||||||
|
except Exception as e :
|
||||||
|
self.s3 = None
|
||||||
|
self.bucket = None
|
||||||
|
print (e)
|
||||||
|
def meta(self,**args):
|
||||||
|
"""
|
||||||
|
:name name of the bucket
|
||||||
|
"""
|
||||||
|
info = self.list(**args)
|
||||||
|
[item.open() for item in info]
|
||||||
|
return [{"name":item.name,"size":item.size} for item in info]
|
||||||
|
def list(self,**args):
|
||||||
|
"""
|
||||||
|
This function will list the content of a bucket, the bucket must be provided by the name
|
||||||
|
:name name of the bucket
|
||||||
|
"""
|
||||||
|
return list(self.s3.get_bucket(args['name']).list())
|
||||||
|
|
||||||
|
|
||||||
|
def buckets(self):
|
||||||
|
#
|
||||||
|
# This function will return all buckets, not sure why but it should be used cautiously
|
||||||
|
# based on why the s3 infrastructure is used
|
||||||
|
#
|
||||||
|
return [item.name for item in self.s3.get_all_buckets()]
|
||||||
|
|
||||||
|
# def buckets(self):
|
||||||
|
pass
|
||||||
|
# """
|
||||||
|
# This function is a wrapper around the bucket list of buckets for s3
|
||||||
|
# """
|
||||||
|
# return self.s3.get_all_buckets()
|
||||||
|
|
||||||
|
|
||||||
|
class Reader(s3) :
|
||||||
|
"""
|
||||||
|
Because s3 contains buckets and files, reading becomes a tricky proposition :
|
||||||
|
- list files if file is None
|
||||||
|
- stream content if file is Not None
|
||||||
|
@TODO: support read from all buckets, think about it
|
||||||
|
"""
|
||||||
|
def __init__(self,**args) :
|
||||||
|
s3.__init__(self,**args)
|
||||||
|
def files(self):
|
||||||
|
r = []
|
||||||
|
try:
|
||||||
|
return [item.name for item in self.bucket if item.size > 0]
|
||||||
|
except Exception as e:
|
||||||
|
pass
|
||||||
|
return r
|
||||||
|
def stream(self,limit=-1):
|
||||||
|
"""
|
||||||
|
At this point we should stream a file from a given bucket
|
||||||
|
"""
|
||||||
|
key = self.bucket.get_key(self.filename.strip())
|
||||||
|
if key is None :
|
||||||
|
yield None
|
||||||
|
else:
|
||||||
|
count = 0
|
||||||
|
with smart_open(key) as remote_file:
|
||||||
|
for line in remote_file:
|
||||||
|
if count == limit and limit > 0 :
|
||||||
|
break
|
||||||
|
yield line
|
||||||
|
count += 1
|
||||||
|
def read(self,**args) :
|
||||||
|
if self.filename is None :
|
||||||
|
#
|
||||||
|
# returning the list of files because no one file was specified.
|
||||||
|
return self.files()
|
||||||
|
else:
|
||||||
|
limit = args['size'] if 'size' in args else -1
|
||||||
|
return self.stream(limit)
|
||||||
|
|
||||||
|
class Writer(s3) :
|
||||||
|
|
||||||
|
def __init__(self,**args) :
|
||||||
|
s3.__init__(self,**args)
|
||||||
|
def mkdir(self,name):
|
||||||
|
"""
|
||||||
|
This function will create a folder in a bucket
|
||||||
|
:name name of the folder
|
||||||
|
"""
|
||||||
|
self.s3.put_object(Bucket=self.bucket_name,key=(name+'/'))
|
||||||
|
def write(self,content):
|
||||||
|
file = StringIO(content.decode("utf8"))
|
||||||
|
self.s3.upload_fileobj(file,self.bucket_name,self.filename)
|
||||||
|
pass
|
||||||
|
|
||||||
|
|
@ -0,0 +1,10 @@
|
||||||
|
"""
|
||||||
|
Steve L. Nyemba, nyemba@gmail.com
|
||||||
|
This namespace implements support for cloud databases couchdb,mongodb, cloudant ...
|
||||||
|
"""
|
||||||
|
from transport.nosql import couchdb
|
||||||
|
from transport.nosql import mongodb
|
||||||
|
# from . import mongodb
|
||||||
|
# from . import couchdb
|
||||||
|
|
||||||
|
cloudant = couchdb
|
||||||
|
|
@ -0,0 +1,213 @@
|
||||||
|
"""
|
||||||
|
Data-Transport
|
||||||
|
Steve L. Nyemba, The Phi Technology
|
||||||
|
|
||||||
|
This file is a wrapper around couchdb using IBM Cloudant SDK that has an interface to couchdb
|
||||||
|
|
||||||
|
"""
|
||||||
|
import cloudant
|
||||||
|
import json
|
||||||
|
import sys
|
||||||
|
# from transport.common import Reader, Writer
|
||||||
|
from datetime import datetime
|
||||||
|
|
||||||
|
|
||||||
|
class Couch:
|
||||||
|
"""
|
||||||
|
This class is a wrapper for read/write against couchdb. The class captures common operations for read/write.
|
||||||
|
@param url host & port reference default http://localhost:5984
|
||||||
|
@param doc user id involved
|
||||||
|
@param dbname database name (target)
|
||||||
|
"""
|
||||||
|
def __init__(self,**args):
|
||||||
|
url = args['url'] if 'url' in args else 'http://localhost:5984'
|
||||||
|
self._id = args['doc']
|
||||||
|
dbname = args['dbname']
|
||||||
|
if 'username' not in args and 'password' not in args :
|
||||||
|
self.server = cloudant.CouchDB(None,None,url=url)
|
||||||
|
else:
|
||||||
|
self.server = cloudant.CouchDB(args['username'],args['password'],url=url)
|
||||||
|
self.server.connect()
|
||||||
|
|
||||||
|
if dbname in self.server.all_dbs() :
|
||||||
|
self.dbase = self.server.get(dbname,dbname,True)
|
||||||
|
#
|
||||||
|
# @TODO Check if the database exists ...
|
||||||
|
#
|
||||||
|
doc = cloudant.document.Document(self.dbase,self._id) #self.dbase.get(self._id)
|
||||||
|
if not doc.exists():
|
||||||
|
doc = self.dbase.create_document({"_id":self._id})
|
||||||
|
doc.save()
|
||||||
|
else:
|
||||||
|
self.dbase = None
|
||||||
|
"""
|
||||||
|
Insuring the preconditions are met for processing
|
||||||
|
"""
|
||||||
|
def isready(self):
|
||||||
|
p = self.server.metadata() != {}
|
||||||
|
if p == False or not self.dbase:
|
||||||
|
return False
|
||||||
|
#
|
||||||
|
# At this point we are sure that the server is connected
|
||||||
|
# We are also sure that the database actually exists
|
||||||
|
#
|
||||||
|
doc = cloudant.document.Document(self.dbase,self._id)
|
||||||
|
# q = self.dbase.all_docs(key=self._id)['rows']
|
||||||
|
# if not q :
|
||||||
|
if not doc.exists():
|
||||||
|
return False
|
||||||
|
return True
|
||||||
|
|
||||||
|
def view(self,**args):
|
||||||
|
"""
|
||||||
|
The function will execute a view (provivded a user is authenticated)
|
||||||
|
:id design document _design/xxxx (provide full name with _design prefix)
|
||||||
|
:view_name name of the view i.e
|
||||||
|
:key(s) key(s) to be used to filter the content
|
||||||
|
"""
|
||||||
|
document = cloudant.design_document.DesignDocument(self.dbase,args['id'])
|
||||||
|
document.fetch()
|
||||||
|
params = {'group_level':1,'group':True}
|
||||||
|
if 'key' in args :
|
||||||
|
params ['key'] = args['key']
|
||||||
|
elif 'keys' in args :
|
||||||
|
params['keys'] = args['keys']
|
||||||
|
return document.get_view(args['view_name'])(**params)['rows']
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
class Reader(Couch):
|
||||||
|
"""
|
||||||
|
This function will read an attachment from couchdb and return it to calling code. The attachment must have been placed before hand (otherwise oops)
|
||||||
|
@T: Account for security & access control
|
||||||
|
"""
|
||||||
|
def __init__(self,**args):
|
||||||
|
"""
|
||||||
|
@param filename filename (attachment)
|
||||||
|
"""
|
||||||
|
#
|
||||||
|
# setting the basic parameters for
|
||||||
|
Couch.__init__(self,**args)
|
||||||
|
if 'filename' in args :
|
||||||
|
self.filename = args['filename']
|
||||||
|
else:
|
||||||
|
self.filename = None
|
||||||
|
|
||||||
|
|
||||||
|
def stream(self):
|
||||||
|
#
|
||||||
|
# @TODO Need to get this working ...
|
||||||
|
#
|
||||||
|
document = cloudant.document.Document(self.dbase,self._id)
|
||||||
|
# content = self.dbase.fetch_attachment(self._id,self.filename).split('\n') ;
|
||||||
|
content = self.get_attachment(self.filename)
|
||||||
|
for row in content:
|
||||||
|
yield row
|
||||||
|
|
||||||
|
def read(self,**args):
|
||||||
|
if self.filename is not None:
|
||||||
|
self.stream()
|
||||||
|
else:
|
||||||
|
return self.basic_read()
|
||||||
|
def basic_read(self):
|
||||||
|
document = cloudant.document.Document(self.dbase,self._id)
|
||||||
|
|
||||||
|
# document = self.dbase.get(self._id)
|
||||||
|
if document.exists() :
|
||||||
|
document.fetch()
|
||||||
|
document = dict(document)
|
||||||
|
del document['_rev']
|
||||||
|
else:
|
||||||
|
document = {}
|
||||||
|
return document
|
||||||
|
|
||||||
|
class Writer(Couch):
|
||||||
|
"""
|
||||||
|
This class will write on a couchdb document provided a scope
|
||||||
|
The scope is the attribute that will be on the couchdb document
|
||||||
|
"""
|
||||||
|
def __init__(self,**args):
|
||||||
|
"""
|
||||||
|
@param uri host & port reference
|
||||||
|
@param uid user id involved
|
||||||
|
@param filename filename (attachment)
|
||||||
|
@param dbname database name (target)
|
||||||
|
"""
|
||||||
|
|
||||||
|
super().__init__(self,**args)
|
||||||
|
def set (self,info):
|
||||||
|
document = cloudant.document.Document(self.dbase,self._id)
|
||||||
|
if document.exists() :
|
||||||
|
keys = list(set(document.keys()) - set(['_id','_rev','_attachments']))
|
||||||
|
for id in keys :
|
||||||
|
document.field_set(document,id,None)
|
||||||
|
for id in info :
|
||||||
|
value = info[id]
|
||||||
|
document.info(document,id,value)
|
||||||
|
|
||||||
|
document.save()
|
||||||
|
pass
|
||||||
|
else:
|
||||||
|
_document = dict({"_id":self._id},**args)
|
||||||
|
document.create_document(_document)
|
||||||
|
def write(self,info):
|
||||||
|
"""
|
||||||
|
write a given attribute to a document database
|
||||||
|
@info object to be written to the to an attribute. this
|
||||||
|
"""
|
||||||
|
|
||||||
|
# document = self.dbase.get(self._id)
|
||||||
|
document = cloudant.document.Document(self.dbase,self._id) #.get(self._id)
|
||||||
|
if document.exists() is False :
|
||||||
|
document = self.dbase.create_document({"_id":self._id})
|
||||||
|
# label = params['label']
|
||||||
|
# row = params['row']
|
||||||
|
# if label not in document :
|
||||||
|
# document[label] = []
|
||||||
|
# document[label].append(row)
|
||||||
|
for key in info :
|
||||||
|
if key in document and type(document[key]) == list :
|
||||||
|
document[key] += info[key]
|
||||||
|
else:
|
||||||
|
document[key] = info[key]
|
||||||
|
|
||||||
|
document.save()
|
||||||
|
# self.dbase.bulk_docs([document])
|
||||||
|
# self.dbase.save_doc(document)
|
||||||
|
|
||||||
|
def upload(self,**args):
|
||||||
|
"""
|
||||||
|
:param name name of the file to be uploaded
|
||||||
|
:param data content of the file (binary or text)
|
||||||
|
:param content_type (default)
|
||||||
|
"""
|
||||||
|
mimetype = args['content_type'] if 'content_type' in args else 'text/plain'
|
||||||
|
document = cloudant.document.Document(self.dbase,self.uid)
|
||||||
|
document.put_attachment(self.dbase,args['filename'],mimetype,args['content'])
|
||||||
|
document.save()
|
||||||
|
|
||||||
|
def archive(self,params=None):
|
||||||
|
"""
|
||||||
|
This function will archive the document onto itself.
|
||||||
|
"""
|
||||||
|
# document = self.dbase.all_docs(self._id,include_docs=True)
|
||||||
|
document = cloudant.document.Document(self.dbase,self.filename)
|
||||||
|
document.fetch()
|
||||||
|
content = {}
|
||||||
|
# _doc = {}
|
||||||
|
for id in document:
|
||||||
|
if id not in ['_id','_rev','_attachments'] :
|
||||||
|
content[id] = document[id]
|
||||||
|
del document[id]
|
||||||
|
|
||||||
|
content = json.dumps(content)
|
||||||
|
# document= _doc
|
||||||
|
now = str(datetime.today())
|
||||||
|
|
||||||
|
name = '-'.join([document['_id'] , now,'.json'])
|
||||||
|
self.upload(filename=name,data=content,content_type='application/json')
|
||||||
|
# self.dbase.bulk_docs([document])
|
||||||
|
# self.dbase.put_attachment(document,content,name,'application/json')
|
||||||
|
# document.put_attachment(self.dbase,name,'application/json',content)
|
||||||
|
# document.save()
|
||||||
|
|
@ -0,0 +1,242 @@
|
||||||
|
"""
|
||||||
|
Data Transport - 1.0
|
||||||
|
Steve L. Nyemba, The Phi Technology LLC
|
||||||
|
|
||||||
|
This file is a wrapper around mongodb for reading/writing content against a mongodb server and executing views (mapreduce)
|
||||||
|
"""
|
||||||
|
from pymongo import MongoClient
|
||||||
|
import bson
|
||||||
|
from bson.objectid import ObjectId
|
||||||
|
from bson.binary import Binary
|
||||||
|
# import nujson as json
|
||||||
|
from datetime import datetime
|
||||||
|
import pandas as pd
|
||||||
|
import numpy as np
|
||||||
|
import gridfs
|
||||||
|
import sys
|
||||||
|
import json
|
||||||
|
import re
|
||||||
|
from multiprocessing import Lock, RLock
|
||||||
|
from transport.common import IEncoder
|
||||||
|
|
||||||
|
class Mongo :
|
||||||
|
lock = RLock()
|
||||||
|
"""
|
||||||
|
Basic mongodb functions are captured here
|
||||||
|
"""
|
||||||
|
def __init__(self,**args):
|
||||||
|
"""
|
||||||
|
:dbname database name/identifier
|
||||||
|
:host host and port of the database by default localhost:27017
|
||||||
|
:username username for authentication
|
||||||
|
:password password for current user
|
||||||
|
"""
|
||||||
|
self.host = 'localhost' if 'host' not in args else args['host']
|
||||||
|
self.mechanism= 'SCRAM-SHA-256' if 'mechanism' not in args else args['mechanism']
|
||||||
|
# authSource=(args['authSource'] if 'authSource' in args else self.dbname)
|
||||||
|
self._lock = False if 'lock' not in args else args['lock']
|
||||||
|
self.dbname = None
|
||||||
|
username = password = None
|
||||||
|
if 'auth_file' in args :
|
||||||
|
_info = json.loads((open(args['auth_file'])).read())
|
||||||
|
|
||||||
|
|
||||||
|
else:
|
||||||
|
_info = {}
|
||||||
|
_args = dict(args,**_info)
|
||||||
|
_map = {'dbname':'db','database':'db','table':'uid','collection':'uid','col':'uid','doc':'uid'}
|
||||||
|
for key in _args :
|
||||||
|
if key in ['username','password'] :
|
||||||
|
username = _args['username'] if key=='username' else username
|
||||||
|
password = _args['password'] if key == 'password' else password
|
||||||
|
continue
|
||||||
|
value = _args[key]
|
||||||
|
if key in _map :
|
||||||
|
key = _map[key]
|
||||||
|
|
||||||
|
self.setattr(key,value)
|
||||||
|
#
|
||||||
|
# Let us perform aliasing in order to remain backwards compatible
|
||||||
|
|
||||||
|
self.dbname = self.db if hasattr(self,'db')else self.dbname
|
||||||
|
self.collection = _args['table'] if 'table' in _args else (_args['doc'] if 'doc' in _args else (_args['collection'] if 'collection' in _args else None))
|
||||||
|
if username and password :
|
||||||
|
self.client = MongoClient(self.host,
|
||||||
|
username=username,
|
||||||
|
password=password ,
|
||||||
|
authSource=self.authSource,
|
||||||
|
authMechanism=self.mechanism)
|
||||||
|
|
||||||
|
else:
|
||||||
|
self.client = MongoClient(self.host,maxPoolSize=10000)
|
||||||
|
|
||||||
|
self.db = self.client[self.dbname]
|
||||||
|
|
||||||
|
def isready(self):
|
||||||
|
p = self.dbname in self.client.list_database_names()
|
||||||
|
q = self.collection in self.client[self.dbname].list_collection_names()
|
||||||
|
return p and q
|
||||||
|
def setattr(self,key,value):
|
||||||
|
_allowed = ['host','port','db','doc','collection','authSource','mechanism']
|
||||||
|
if key in _allowed :
|
||||||
|
setattr(self,key,value)
|
||||||
|
pass
|
||||||
|
def close(self):
|
||||||
|
self.client.close()
|
||||||
|
def meta(self,**_args):
|
||||||
|
return []
|
||||||
|
class Reader(Mongo):
|
||||||
|
"""
|
||||||
|
This class will read from a mongodb data store and return the content of a document (not a collection)
|
||||||
|
"""
|
||||||
|
def __init__(self,**args):
|
||||||
|
Mongo.__init__(self,**args)
|
||||||
|
def read(self,**args):
|
||||||
|
|
||||||
|
if 'mongo' in args or 'cmd' in args or 'pipeline' in args:
|
||||||
|
#
|
||||||
|
# @TODO:
|
||||||
|
cmd = {}
|
||||||
|
if 'aggregate' not in cmd and 'aggregate' not in args:
|
||||||
|
cmd['aggregate'] = self.collection
|
||||||
|
elif 'aggregate' in args :
|
||||||
|
cmd['aggregate'] = args['aggregate']
|
||||||
|
if 'pipeline' in args :
|
||||||
|
cmd['pipeline']= args['pipeline']
|
||||||
|
|
||||||
|
if 'pipeline' not in args or 'aggregate' not in cmd :
|
||||||
|
cmd = args['mongo'] if 'mongo' in args else args['cmd']
|
||||||
|
if "aggregate" in cmd :
|
||||||
|
if "allowDiskUse" not in cmd :
|
||||||
|
cmd["allowDiskUse"] = True
|
||||||
|
if "cursor" not in cmd :
|
||||||
|
cmd["cursor"] = {}
|
||||||
|
r = []
|
||||||
|
out = self.db.command(cmd)
|
||||||
|
#@TODO: consider using a yield (generator) works wonders
|
||||||
|
while True :
|
||||||
|
if 'values' in out :
|
||||||
|
r += out['values']
|
||||||
|
if 'cursor' in out :
|
||||||
|
key = 'firstBatch' if 'firstBatch' in out['cursor'] else 'nextBatch'
|
||||||
|
else:
|
||||||
|
key = 'n'
|
||||||
|
if 'cursor' in out and out['cursor'][key] :
|
||||||
|
r += list(out['cursor'][key])
|
||||||
|
elif key in out and out[key]:
|
||||||
|
r.append (out[key])
|
||||||
|
# yield out['cursor'][key]
|
||||||
|
if key not in ['firstBatch','nextBatch'] or ('cursor' in out and out['cursor']['id'] == 0) :
|
||||||
|
break
|
||||||
|
else:
|
||||||
|
out = self.db.command({"getMore":out['cursor']['id'],"collection":out['cursor']['ns'].split(".")[-1]})
|
||||||
|
|
||||||
|
|
||||||
|
return pd.DataFrame(r)
|
||||||
|
else:
|
||||||
|
|
||||||
|
|
||||||
|
if 'table' in args or 'collection' in args :
|
||||||
|
if 'table' in args:
|
||||||
|
_uid = args['table']
|
||||||
|
elif 'collection' in args :
|
||||||
|
_uid = args['collection']
|
||||||
|
else:
|
||||||
|
_uid = self.collection
|
||||||
|
else:
|
||||||
|
_uid = self.collection
|
||||||
|
collection = self.db[_uid]
|
||||||
|
_filter = args['filter'] if 'filter' in args else {}
|
||||||
|
_df = pd.DataFrame(collection.find(_filter))
|
||||||
|
columns = _df.columns.tolist()[1:]
|
||||||
|
return _df[columns]
|
||||||
|
def view(self,**args):
|
||||||
|
"""
|
||||||
|
This function is designed to execute a view (map/reduce) operation
|
||||||
|
"""
|
||||||
|
pass
|
||||||
|
class Writer(Mongo):
|
||||||
|
"""
|
||||||
|
This class is designed to write to a mongodb collection within a database
|
||||||
|
"""
|
||||||
|
def __init__(self,**args):
|
||||||
|
Mongo.__init__(self,**args)
|
||||||
|
def upload(self,**args) :
|
||||||
|
"""
|
||||||
|
This function will upload a file to the current database (using GridFS)
|
||||||
|
:param data binary stream/text to be stored
|
||||||
|
:param filename filename to be used
|
||||||
|
:param encoding content_encoding (default utf-8)
|
||||||
|
|
||||||
|
"""
|
||||||
|
if 'encoding' not in args :
|
||||||
|
args['encoding'] = 'utf-8'
|
||||||
|
gfs = GridFS(self.db)
|
||||||
|
gfs.put(**args)
|
||||||
|
|
||||||
|
def archive(self):
|
||||||
|
"""
|
||||||
|
This function will archive documents to the
|
||||||
|
"""
|
||||||
|
collection = self.db[self.collection]
|
||||||
|
rows = list(collection.find())
|
||||||
|
for row in rows :
|
||||||
|
if type(row['_id']) == ObjectId :
|
||||||
|
row['_id'] = str(row['_id'])
|
||||||
|
stream = Binary(json.dumps(collection,cls=IEncoder).encode())
|
||||||
|
collection.delete_many({})
|
||||||
|
now = "-".join([str(datetime.now().year()),str(datetime.now().month), str(datetime.now().day)])
|
||||||
|
name = ".".join([self.collection,'archive',now])+".json"
|
||||||
|
description = " ".join([self.collection,'archive',str(len(rows))])
|
||||||
|
self.upload(filename=name,data=stream,description=description,content_type='application/json')
|
||||||
|
# gfs = GridFS(self.db)
|
||||||
|
# gfs.put(filename=name,description=description,data=stream,encoding='utf-8')
|
||||||
|
# self.write({{"filename":name,"file":stream,"description":descriptions}})
|
||||||
|
|
||||||
|
|
||||||
|
pass
|
||||||
|
|
||||||
|
def write(self,info,**_args):
|
||||||
|
"""
|
||||||
|
This function will write to a given collection i.e add a record to a collection (no updates)
|
||||||
|
@param info new record in the collection to be added
|
||||||
|
"""
|
||||||
|
# document = self.db[self.collection].find()
|
||||||
|
#collection = self.db[self.collection]
|
||||||
|
# if type(info) == list :
|
||||||
|
# self.db[self.collection].insert_many(info)
|
||||||
|
# else:
|
||||||
|
try:
|
||||||
|
if 'table' in _args or 'collection' in _args :
|
||||||
|
_uid = _args['table'] if 'table' in _args else _args['collection']
|
||||||
|
else:
|
||||||
|
_uid = self.collection if 'doc' not in _args else _args['doc']
|
||||||
|
if self._lock :
|
||||||
|
Mongo.lock.acquire()
|
||||||
|
if type(info) == list or type(info) == pd.DataFrame :
|
||||||
|
info if type(info) == list else info.to_dict(orient='records')
|
||||||
|
info = json.loads(json.dumps(info,cls=IEncoder))
|
||||||
|
self.db[_uid].insert_many(info)
|
||||||
|
else:
|
||||||
|
self.db[_uid].insert_one(json.loads(json.dumps(info,cls=IEncoder)))
|
||||||
|
finally:
|
||||||
|
if self._lock :
|
||||||
|
Mongo.lock.release()
|
||||||
|
def set(self,document):
|
||||||
|
"""
|
||||||
|
if no identifier is provided the function will delete the entire collection and set the new document.
|
||||||
|
Please use this function with great care (archive the content first before using it... for safety)
|
||||||
|
"""
|
||||||
|
|
||||||
|
collection = self.db[self.collection]
|
||||||
|
if collection.count_document() > 0 and '_id' in document:
|
||||||
|
id = document['_id']
|
||||||
|
del document['_id']
|
||||||
|
collection.find_one_and_replace({'_id':id},document)
|
||||||
|
else:
|
||||||
|
collection.delete_many({})
|
||||||
|
self.write(info)
|
||||||
|
def close(self):
|
||||||
|
Mongo.close(self)
|
||||||
|
# collecton.update_one({"_id":self.collection},document,True)
|
||||||
|
|
||||||
|
|
@ -0,0 +1 @@
|
||||||
|
from . import files, http, rabbitmq, callback, files
|
||||||
|
|
@ -0,0 +1,45 @@
|
||||||
|
import queue
|
||||||
|
from threading import Thread, Lock
|
||||||
|
from transport.common import Reader,Writer
|
||||||
|
import numpy as np
|
||||||
|
import pandas as pd
|
||||||
|
|
||||||
|
class Writer :
|
||||||
|
lock = Lock()
|
||||||
|
_queue = {'default':queue.Queue()}
|
||||||
|
def __init__(self,**_args):
|
||||||
|
self._cache = {}
|
||||||
|
self._callback = _args['callback'] if 'callback' in _args else None
|
||||||
|
self._id = _args['id'] if 'id' in _args else 'default'
|
||||||
|
if self._id not in Writer._queue :
|
||||||
|
Writer._queue[self._id] = queue.Queue()
|
||||||
|
thread = Thread(target=self._forward)
|
||||||
|
thread.start()
|
||||||
|
def _forward(self):
|
||||||
|
_q = Writer._queue[self._id]
|
||||||
|
_data = _q.get()
|
||||||
|
_q.task_done()
|
||||||
|
self._callback(_data)
|
||||||
|
|
||||||
|
def has(self,**_args) :
|
||||||
|
return self._callback is not None
|
||||||
|
|
||||||
|
|
||||||
|
def close(self):
|
||||||
|
"""
|
||||||
|
This will empty the queue and have it ready for another operation
|
||||||
|
"""
|
||||||
|
_q = Writer._queue[self._id]
|
||||||
|
with _q.mutex:
|
||||||
|
_q.queue.clear()
|
||||||
|
_q.all_tasks_done.notify_all()
|
||||||
|
|
||||||
|
def write(self,_data,**_args):
|
||||||
|
_id = _args['id'] if 'id' in _args else self._id
|
||||||
|
|
||||||
|
_q = Writer._queue[_id]
|
||||||
|
_q.put(_data)
|
||||||
|
_q.join()
|
||||||
|
|
||||||
|
|
||||||
|
# self.callback = print
|
||||||
|
|
@ -0,0 +1,7 @@
|
||||||
|
from . import callback
|
||||||
|
|
||||||
|
|
||||||
|
class Writer (callback.Writer):
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(callback=print)
|
||||||
|
|
||||||
|
|
@ -0,0 +1,68 @@
|
||||||
|
"""
|
||||||
|
This file is a wrapper around pandas built-in functionalities to handle character delimited files
|
||||||
|
"""
|
||||||
|
import pandas as pd
|
||||||
|
import numpy as np
|
||||||
|
import os
|
||||||
|
class File :
|
||||||
|
def __init__(self,**params):
|
||||||
|
"""
|
||||||
|
|
||||||
|
@param path absolute path of the file to be read
|
||||||
|
"""
|
||||||
|
self.path = params['path'] if 'path' in params else None
|
||||||
|
self.delimiter = params['delimiter'] if 'delimiter' in params else ','
|
||||||
|
|
||||||
|
def isready(self):
|
||||||
|
return os.path.exists(self.path)
|
||||||
|
def meta(self,**_args):
|
||||||
|
return []
|
||||||
|
|
||||||
|
class Reader (File):
|
||||||
|
"""
|
||||||
|
This class is designed to read data from disk (location on hard drive)
|
||||||
|
@pre : isready() == True
|
||||||
|
"""
|
||||||
|
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
|
||||||
|
def read(self,**args):
|
||||||
|
_path = self.path if 'path' not in args else args['path']
|
||||||
|
_delimiter = self.delimiter if 'delimiter' not in args else args['delimiter']
|
||||||
|
return pd.read_csv(_path,delimiter=self.delimiter)
|
||||||
|
def stream(self,**args):
|
||||||
|
raise Exception ("streaming needs to be implemented")
|
||||||
|
class Writer (File):
|
||||||
|
|
||||||
|
"""
|
||||||
|
This function writes output to disk in a designated location. The function will write a text to a text file
|
||||||
|
- If a delimiter is provided it will use that to generate a xchar-delimited file
|
||||||
|
- If not then the object will be dumped as is
|
||||||
|
"""
|
||||||
|
# THREAD_LOCK = RLock()
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
self._mode = 'w' if 'mode' not in _args else _args['mode']
|
||||||
|
|
||||||
|
def write(self,info,**_args):
|
||||||
|
"""
|
||||||
|
This function writes a record to a designated file
|
||||||
|
@param label <passed|broken|fixed|stats>
|
||||||
|
@param row row to be written
|
||||||
|
"""
|
||||||
|
try:
|
||||||
|
|
||||||
|
_delim = self._delimiter if 'delimiter' not in _args else _args['delimiter']
|
||||||
|
_path = self._path if 'path' not in _args else _args['path']
|
||||||
|
_mode = self._mode if 'mode' not in _args else _args['mode']
|
||||||
|
info.to_csv(_path,index=False,sep=_delim)
|
||||||
|
|
||||||
|
pass
|
||||||
|
except Exception as e:
|
||||||
|
#
|
||||||
|
# Not sure what should be done here ...
|
||||||
|
pass
|
||||||
|
finally:
|
||||||
|
# DiskWriter.THREAD_LOCK.release()
|
||||||
|
pass
|
||||||
|
|
@ -0,0 +1,88 @@
|
||||||
|
from flask import request, session
|
||||||
|
from datetime import datetime
|
||||||
|
import re
|
||||||
|
# from transport.common import Reader, Writer
|
||||||
|
import json
|
||||||
|
import requests
|
||||||
|
from io import StringIO
|
||||||
|
import pandas as pd
|
||||||
|
|
||||||
|
|
||||||
|
class Reader:
|
||||||
|
"""
|
||||||
|
This class is designed to read data from an Http request file handler provided to us by flask
|
||||||
|
The file will be heald in memory and processed accordingly
|
||||||
|
NOTE: This is inefficient and can crash a micro-instance (becareful)
|
||||||
|
"""
|
||||||
|
|
||||||
|
def __init__(self,**_args):
|
||||||
|
self._url = _args['url']
|
||||||
|
self._headers = None if 'headers' not in _args else _args['headers']
|
||||||
|
|
||||||
|
# def isready(self):
|
||||||
|
# return self.file_length > 0
|
||||||
|
def format(self,_response):
|
||||||
|
_mimetype= _response.headers['Content-Type']
|
||||||
|
if _mimetype == 'text/csv' or 'text/csv':
|
||||||
|
_content = _response.text
|
||||||
|
return pd.read_csv(StringIO(_content))
|
||||||
|
#
|
||||||
|
# @TODO: Add support for excel, JSON and other file formats that fit into a data-frame
|
||||||
|
#
|
||||||
|
|
||||||
|
return _response.text
|
||||||
|
def read(self,**_args):
|
||||||
|
if self._headers :
|
||||||
|
r = requests.get(self._url,headers = self._headers)
|
||||||
|
else:
|
||||||
|
r = requests.get(self._url,headers = self._headers)
|
||||||
|
return self.format(r)
|
||||||
|
|
||||||
|
class Writer:
|
||||||
|
"""
|
||||||
|
This class is designed to submit data to an endpoint (url)
|
||||||
|
"""
|
||||||
|
def __init__(self,**_args):
|
||||||
|
"""
|
||||||
|
@param key required session key
|
||||||
|
"""
|
||||||
|
self._url = _args['url']
|
||||||
|
self._name = _args['name']
|
||||||
|
self._method = 'post' if 'method' not in _args else _args['method']
|
||||||
|
|
||||||
|
# self.session = params['queue']
|
||||||
|
# self.session['sql'] = []
|
||||||
|
# self.session['csv'] = []
|
||||||
|
# self.tablename = re.sub('..+$','',params['filename'])
|
||||||
|
# self.session['uid'] = params['uid']
|
||||||
|
#self.xchar = params['xchar']
|
||||||
|
|
||||||
|
|
||||||
|
def format_sql(self,row):
|
||||||
|
values = "','".join([col.replace('"','').replace("'",'') for col in row])
|
||||||
|
return "".join(["INSERT INTO :table VALUES('",values,"');\n"]).replace(':table',self.tablename)
|
||||||
|
def isready(self):
|
||||||
|
return True
|
||||||
|
def write(self,_data,**_args):
|
||||||
|
#
|
||||||
|
#
|
||||||
|
_method = self._method if 'method' not in _args else _args['method']
|
||||||
|
_method = _method.lower()
|
||||||
|
_mimetype = 'text/csv'
|
||||||
|
if type(_data) == dict :
|
||||||
|
_mimetype = 'application/json'
|
||||||
|
_content = _data
|
||||||
|
else:
|
||||||
|
_content = _data.to_dict(orient='records')
|
||||||
|
_headers = {'Content-Type':_mimetype}
|
||||||
|
_pointer = getattr(requests,_method)
|
||||||
|
|
||||||
|
_pointer ({self._name:_content},headers=_headers)
|
||||||
|
|
||||||
|
|
||||||
|
# label = params['label']
|
||||||
|
# row = params ['row']
|
||||||
|
|
||||||
|
# if label == 'usable':
|
||||||
|
# self.session['csv'].append(self.format(row,','))
|
||||||
|
# self.session['sql'].append(self.format_sql(row))
|
||||||
|
|
@ -0,0 +1,272 @@
|
||||||
|
"""
|
||||||
|
Data Transport - 1.0
|
||||||
|
Steve L. Nyemba, The Phi Technology LLC
|
||||||
|
|
||||||
|
This file is a wrapper around rabbitmq server for reading and writing content to a queue (exchange)
|
||||||
|
|
||||||
|
"""
|
||||||
|
import pika
|
||||||
|
from datetime import datetime
|
||||||
|
import re
|
||||||
|
import json
|
||||||
|
import os
|
||||||
|
import sys
|
||||||
|
# if sys.version_info[0] > 2 :
|
||||||
|
# from transport.common import Reader, Writer
|
||||||
|
# else:
|
||||||
|
# from common import Reader, Writer
|
||||||
|
import json
|
||||||
|
from multiprocessing import RLock
|
||||||
|
class MessageQueue:
|
||||||
|
"""
|
||||||
|
This class hierarchy is designed to handle interactions with a queue server using pika framework (our tests are based on rabbitmq)
|
||||||
|
:host
|
||||||
|
:xid identifier of the exchange
|
||||||
|
:qid identifier of the queue
|
||||||
|
"""
|
||||||
|
def __init__(self,**params):
|
||||||
|
self.host= 'localhost' if 'host' not in params else params['host'] #-- location of the queue server
|
||||||
|
self.port= 5672 if 'port' not in params else params['port']
|
||||||
|
self.virtual_host = '/' if 'vhost' not in params else params['vhost']
|
||||||
|
self.exchange = params['exchange'] if 'exchange' in params else 'amq.direct' #-- exchange
|
||||||
|
self.queue = params['queue'] if 'queue' in params else 'demo'
|
||||||
|
self.connection = None
|
||||||
|
self.channel = None
|
||||||
|
|
||||||
|
self.name = self.__class__.__name__.lower() if 'name' not in params else params['name']
|
||||||
|
|
||||||
|
username = password = None
|
||||||
|
if 'username' in params :
|
||||||
|
username = params['username']
|
||||||
|
password = params['password']
|
||||||
|
if 'auth_file' in params :
|
||||||
|
_info = json.loads((open(params['auth_file'])).read())
|
||||||
|
username=_info['username']
|
||||||
|
password=_info['password']
|
||||||
|
self.virtual_host = _info['virtual_host'] if 'virtual_host' in _info else self.virtual_host
|
||||||
|
self.exchange = _info['exchange'] if 'exchange' in _info else self.exchange
|
||||||
|
self.queue = _info['queue'] if 'queue' in _info else self.queue
|
||||||
|
|
||||||
|
self.credentials= pika.PlainCredentials('guest','guest')
|
||||||
|
if 'username' in params :
|
||||||
|
self.credentials = pika.PlainCredentials(
|
||||||
|
params['username'],
|
||||||
|
('' if 'password' not in params else params['password'])
|
||||||
|
)
|
||||||
|
|
||||||
|
def init(self,label=None):
|
||||||
|
properties = pika.ConnectionParameters(host=self.host,port=self.port,virtual_host=self.virtual_host,
|
||||||
|
client_properties={'connection_name':self.name},
|
||||||
|
credentials=self.credentials)
|
||||||
|
self.connection = pika.BlockingConnection(properties)
|
||||||
|
self.channel = self.connection.channel()
|
||||||
|
self.info = self.channel.exchange_declare(exchange=self.exchange,exchange_type='direct',durable=True)
|
||||||
|
if label is None:
|
||||||
|
self.qhandler = self.channel.queue_declare(queue=self.queue,durable=True)
|
||||||
|
else:
|
||||||
|
self.qhandler = self.channel.queue_declare(queue=label,durable=True)
|
||||||
|
|
||||||
|
self.channel.queue_bind(exchange=self.exchange,queue=self.qhandler.method.queue)
|
||||||
|
|
||||||
|
def isready(self):
|
||||||
|
#self.init()
|
||||||
|
resp = self.connection is not None and self.connection.is_open
|
||||||
|
# self.close()
|
||||||
|
return resp
|
||||||
|
def finalize(self):
|
||||||
|
pass
|
||||||
|
def close(self):
|
||||||
|
if self.connection.is_closed == False :
|
||||||
|
self.channel.close()
|
||||||
|
self.connection.close()
|
||||||
|
|
||||||
|
class Writer(MessageQueue):
|
||||||
|
"""
|
||||||
|
This class is designed to publish content to an AMQP (Rabbitmq)
|
||||||
|
The class will rely on pika to implement this functionality
|
||||||
|
|
||||||
|
We will publish information to a given queue for a given exchange
|
||||||
|
"""
|
||||||
|
def __init__(self,**params):
|
||||||
|
#self.host= params['host']
|
||||||
|
#self.exchange = params['uid']
|
||||||
|
#self.queue = params['queue']
|
||||||
|
MessageQueue.__init__(self,**params);
|
||||||
|
self.init()
|
||||||
|
def write(self,data,_type='text/plain'):
|
||||||
|
"""
|
||||||
|
This function writes a stream of data to the a given queue
|
||||||
|
@param object object to be written (will be converted to JSON)
|
||||||
|
@TODO: make this less chatty
|
||||||
|
"""
|
||||||
|
|
||||||
|
stream = json.dumps(data) if isinstance(data,dict) else data
|
||||||
|
self.channel.basic_publish(
|
||||||
|
exchange=self.exchange,
|
||||||
|
routing_key=self.queue,
|
||||||
|
body=stream,
|
||||||
|
properties=pika.BasicProperties(content_type=_type,delivery_mode=2)
|
||||||
|
);
|
||||||
|
# self.close()
|
||||||
|
|
||||||
|
def flush(self):
|
||||||
|
self.init()
|
||||||
|
_mode = 1 #-- Non persistent
|
||||||
|
self.channel.queue_delete( queue=self.queue);
|
||||||
|
self.close()
|
||||||
|
|
||||||
|
class Reader(MessageQueue):
|
||||||
|
"""
|
||||||
|
This class will read from a queue provided an exchange, queue and host
|
||||||
|
@TODO: Account for security and virtualhosts
|
||||||
|
"""
|
||||||
|
|
||||||
|
def __init__(self,**params):
|
||||||
|
"""
|
||||||
|
@param host host
|
||||||
|
@param uid exchange identifier
|
||||||
|
@param qid queue identifier
|
||||||
|
"""
|
||||||
|
|
||||||
|
#self.host= params['host']
|
||||||
|
#self.exchange = params['uid']
|
||||||
|
#self.queue = params['qid']
|
||||||
|
MessageQueue.__init__(self,**params);
|
||||||
|
# self.init()
|
||||||
|
self.durable = False if 'durable' not in params else params['durable']
|
||||||
|
# if 'durable' in params :
|
||||||
|
# self.durable = True
|
||||||
|
# else:
|
||||||
|
# self.durable = False
|
||||||
|
self.size = -1
|
||||||
|
self.data = {}
|
||||||
|
# def init(self,qid):
|
||||||
|
|
||||||
|
# properties = pika.ConnectionParameters(host=self.host)
|
||||||
|
# self.connection = pika.BlockingConnection(properties)
|
||||||
|
# self.channel = self.connection.channel()
|
||||||
|
# self.channel.exchange_declare(exchange=self.exchange,type='direct',durable=True)
|
||||||
|
|
||||||
|
# self.info = self.channel.queue_declare(queue=qid,durable=True)
|
||||||
|
|
||||||
|
|
||||||
|
def callback(self,channel,method,header,stream):
|
||||||
|
"""
|
||||||
|
This is the callback function designed to process the data stream from the queue
|
||||||
|
|
||||||
|
"""
|
||||||
|
|
||||||
|
r = []
|
||||||
|
# if re.match("^\{|\[",stream) is not None:
|
||||||
|
if stream.startswith(b'{') or stream.startswith(b'['):
|
||||||
|
r = json.loads(stream)
|
||||||
|
else:
|
||||||
|
|
||||||
|
r = stream
|
||||||
|
|
||||||
|
qid = self.qhandler.method.queue
|
||||||
|
if qid not in self.data :
|
||||||
|
self.data[qid] = []
|
||||||
|
|
||||||
|
self.data[qid].append(r)
|
||||||
|
#
|
||||||
|
# We stop reading when the all the messages of the queue are staked
|
||||||
|
#
|
||||||
|
if self.size == len(self.data[qid]) or len(self.data[qid]) == self.info.method.message_count:
|
||||||
|
self.close()
|
||||||
|
|
||||||
|
def read(self,**args):
|
||||||
|
"""
|
||||||
|
This function will read, the first message from a queue
|
||||||
|
@TODO:
|
||||||
|
Implement channel.basic_get in order to retrieve a single message at a time
|
||||||
|
Have the number of messages retrieved be specified by size (parameter)
|
||||||
|
"""
|
||||||
|
r = {}
|
||||||
|
self.size = -1 if 'size' in args else int(args['size'])
|
||||||
|
#
|
||||||
|
# We enabled the reader to be able to read from several queues (sequentially for now)
|
||||||
|
# The qid parameter will be an array of queues the reader will be reading from
|
||||||
|
#
|
||||||
|
if isinstance(self.queue,str) :
|
||||||
|
self.queue = [self.queue]
|
||||||
|
|
||||||
|
for qid in self.queue:
|
||||||
|
self.init(qid)
|
||||||
|
# r[qid] = []
|
||||||
|
|
||||||
|
if self.qhandler.method.message_count > 0:
|
||||||
|
|
||||||
|
self.channel.basic_consume(queue=qid,on_message_callback=self.callback,auto_ack=False);
|
||||||
|
self.channel.start_consuming()
|
||||||
|
else:
|
||||||
|
|
||||||
|
pass
|
||||||
|
#self.close()
|
||||||
|
# r[qid].append( self.data)
|
||||||
|
|
||||||
|
return self.data
|
||||||
|
class QueueListener(MessageQueue):
|
||||||
|
lock = RLock()
|
||||||
|
"""
|
||||||
|
This class is designed to have an active listener (worker) against a specified Exchange/Queue
|
||||||
|
It is initialized as would any other object and will require a callback function to address the objects returned.
|
||||||
|
"""
|
||||||
|
def __init__(self,**args):
|
||||||
|
MessageQueue.__init__(self,**args)
|
||||||
|
self.listen = self.read
|
||||||
|
self.apply = args['apply'] if 'apply' in args else print
|
||||||
|
self.lock = False if 'lock' not in args else args['lock']
|
||||||
|
|
||||||
|
def finalize(self,channel,ExceptionReason):
|
||||||
|
pass
|
||||||
|
|
||||||
|
def callback(self,channel,method,header,stream) :
|
||||||
|
_info= {}
|
||||||
|
# if re.match("^\{|\[",stream) is not None:
|
||||||
|
|
||||||
|
|
||||||
|
if stream.startswith(b"[") or stream.startswith(b"{"):
|
||||||
|
_info = json.loads(stream)
|
||||||
|
else:
|
||||||
|
|
||||||
|
_info = stream
|
||||||
|
#
|
||||||
|
# At this point we should invoke the apply function with a lock if need be
|
||||||
|
# @TODO: Establish a vocabulary
|
||||||
|
|
||||||
|
if stream == b'QUIT' :
|
||||||
|
# channel.exit()
|
||||||
|
self.close()
|
||||||
|
if self.lock == True :
|
||||||
|
QueueListener.lock.acquire()
|
||||||
|
try:
|
||||||
|
#
|
||||||
|
# In case the user has not specified a function to apply the data against, it will simply be printed
|
||||||
|
#
|
||||||
|
self.apply(_info)
|
||||||
|
except Exception as e:
|
||||||
|
pass
|
||||||
|
if self.lock == True :
|
||||||
|
QueueListener.lock.release()
|
||||||
|
def read(self):
|
||||||
|
|
||||||
|
self.init(self.queue)
|
||||||
|
|
||||||
|
self.channel.basic_consume(self.queue,self.callback,auto_ack=True);
|
||||||
|
self.channel.start_consuming()
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
class Factory :
|
||||||
|
@staticmethod
|
||||||
|
def instance(**_args):
|
||||||
|
"""
|
||||||
|
:param count number of workers
|
||||||
|
:param apply function workers
|
||||||
|
"""
|
||||||
|
_apply = _args['apply']
|
||||||
|
_count = _args['count']
|
||||||
|
for i in np.arange(_count) :
|
||||||
|
_name = _args['name'] if 'name' in _args else 'worker_'+str(i)
|
||||||
|
transport.factory.instance(provider="rabbit",context="listener",apply=_apply,auth_file=_args['auth_file'])
|
||||||
|
|
@ -1,105 +0,0 @@
|
||||||
# from transport.common import Reader, Writer,Console #, factory
|
|
||||||
from transport import disk
|
|
||||||
import sqlite3
|
|
||||||
from transport import s3 as s3
|
|
||||||
from transport import rabbitmq as queue
|
|
||||||
from transport import couch as couch
|
|
||||||
from transport import mongo as mongo
|
|
||||||
from transport import sql as sql
|
|
||||||
from transport import etl as etl
|
|
||||||
from transport import qlistener
|
|
||||||
from transport import bricks
|
|
||||||
from transport import session
|
|
||||||
from transport import nextcloud
|
|
||||||
import psycopg2 as pg
|
|
||||||
import mysql.connector as my
|
|
||||||
from google.cloud import bigquery as bq
|
|
||||||
import nzpy as nz #--- netezza drivers
|
|
||||||
import os
|
|
||||||
|
|
||||||
from info import __version__
|
|
||||||
|
|
||||||
POSTGRESQL = 'postgresql'
|
|
||||||
MONGODB = 'mongodb'
|
|
||||||
HTTP='http'
|
|
||||||
BIGQUERY ='bigquery'
|
|
||||||
FILE = 'file'
|
|
||||||
ETL = 'etl'
|
|
||||||
SQLITE = 'sqlite'
|
|
||||||
SQLITE3= 'sqlite'
|
|
||||||
REDSHIFT = 'redshift'
|
|
||||||
NETEZZA = 'netezza'
|
|
||||||
MYSQL = 'mysql+mysqlconnector'
|
|
||||||
RABBITMQ = 'rabbitmq'
|
|
||||||
MARIADB = 'mariadb'
|
|
||||||
COUCHDB = 'couch'
|
|
||||||
CONSOLE = 'console'
|
|
||||||
ETL = 'etl'
|
|
||||||
TRANSPORT = ETL
|
|
||||||
NEXTCLOUD = 'nextcloud'
|
|
||||||
|
|
||||||
#
|
|
||||||
# synonyms of the above
|
|
||||||
BQ = BIGQUERY
|
|
||||||
MONGO = MONGODB
|
|
||||||
FERRETDB= MONGODB
|
|
||||||
PG = POSTGRESQL
|
|
||||||
PSQL = POSTGRESQL
|
|
||||||
PGSQL = POSTGRESQL
|
|
||||||
S3 = 's3'
|
|
||||||
AWS_S3 = 's3'
|
|
||||||
RABBIT = RABBITMQ
|
|
||||||
|
|
||||||
QLISTENER = 'qlistener'
|
|
||||||
QUEUE = QLISTENER
|
|
||||||
CALLBACK = QLISTENER
|
|
||||||
DATABRICKS= 'databricks+connector'
|
|
||||||
DRIVERS = {PG:pg,REDSHIFT:pg,MYSQL:my,MARIADB:my,NETEZZA:nz,SQLITE:sqlite3}
|
|
||||||
CATEGORIES ={'sql':[NETEZZA,PG,MYSQL,REDSHIFT,SQLITE,MARIADB],'nosql':[MONGODB,COUCHDB],'cloud':[NEXTCLOUD,S3,BIGQUERY,DATABRICKS],'file':[FILE],
|
|
||||||
'queue':[RABBIT,QLISTENER],'memory':[CONSOLE,QUEUE],'http':[HTTP]}
|
|
||||||
|
|
||||||
READ = {'sql':sql.SQLReader,'nosql':{MONGODB:mongo.MongoReader,COUCHDB:couch.CouchReader},
|
|
||||||
'cloud':{BIGQUERY:sql.BigQueryReader,DATABRICKS:bricks.BricksReader,NEXTCLOUD:nextcloud.NextcloudReader},
|
|
||||||
'file':disk.DiskReader,'queue':{RABBIT:queue.QueueReader,QLISTENER:qlistener.qListener},
|
|
||||||
# 'cli':{CONSOLE:Console},'memory':{CONSOLE:Console},'http':session.HttpReader
|
|
||||||
}
|
|
||||||
WRITE = {'sql':sql.SQLWriter,'nosql':{MONGODB:mongo.MongoWriter,COUCHDB:couch.CouchWriter},
|
|
||||||
'cloud':{BIGQUERY:sql.BigQueryWriter,DATABRICKS:bricks.BricksWriter,NEXTCLOUD:nextcloud.NextcloudWriter},
|
|
||||||
'file':disk.DiskWriter,'queue':{RABBIT:queue.QueueWriter,QLISTENER:qlistener.qListener},
|
|
||||||
# 'cli':{CONSOLE:Console},
|
|
||||||
# 'memory':{CONSOLE:Console}, 'http':session.HttpReader
|
|
||||||
|
|
||||||
}
|
|
||||||
# SQL_PROVIDERS = [POSTGRESQL,MYSQL,NETEZZA,MARIADB,SQLITE]
|
|
||||||
PROVIDERS = {
|
|
||||||
FILE:{'read':disk.DiskReader,'write':disk.DiskWriter},
|
|
||||||
SQLITE:{'read':disk.SQLiteReader,'write':disk.SQLiteWriter,'driver':sqlite3},
|
|
||||||
'sqlite3':{'read':disk.SQLiteReader,'write':disk.SQLiteWriter,'driver':sqlite3},
|
|
||||||
|
|
||||||
POSTGRESQL:{'read':sql.SQLReader,'write':sql.SQLWriter,'driver':pg,'default':{'host':'localhost','port':5432}},
|
|
||||||
NETEZZA:{'read':sql.SQLReader,'write':sql.SQLWriter,'driver':nz,'default':{'port':5480}},
|
|
||||||
REDSHIFT:{'read':sql.SQLReader,'write':sql.SQLWriter,'driver':pg,'default':{'host':'localhost','port':5432}},
|
|
||||||
RABBITMQ:{'read':queue.QueueReader,'writer':queue.QueueWriter,'context':queue.QueueListener,'default':{'host':'localhost','port':5432}},
|
|
||||||
|
|
||||||
MYSQL:{'read':sql.SQLReader,'write':sql.SQLWriter,'driver':my,'default':{'host':'localhost','port':3306}},
|
|
||||||
MARIADB:{'read':sql.SQLReader,'write':sql.SQLWriter,'driver':my,'default':{'host':'localhost','port':3306}},
|
|
||||||
|
|
||||||
S3:{'read':s3.s3Reader,'write':s3.s3Writer},
|
|
||||||
BIGQUERY:{'read':sql.BigQueryReader,'write':sql.BigQueryWriter},
|
|
||||||
DATABRICKS:{'read':bricks.BricksReader,'write':bricks.BricksWriter},
|
|
||||||
NEXTCLOUD:{'read':nextcloud.NextcloudReader,'write':nextcloud.NextcloudWriter},
|
|
||||||
|
|
||||||
QLISTENER:{'read':qlistener.qListener,'write':qlistener.qListener,'default':{'host':'localhost','port':5672}},
|
|
||||||
CONSOLE:{'read':qlistener.Console,"write":qlistener.Console},
|
|
||||||
HTTP:{'read':session.HttpReader,'write':session.HttpWriter},
|
|
||||||
|
|
||||||
MONGODB:{'read':mongo.MongoReader,'write':mongo.MongoWriter,'default':{'port':27017,'host':'localhost'}},
|
|
||||||
COUCHDB:{'read':couch.CouchReader,'writer':couch.CouchWriter,'default':{'host':'localhost','port':5984}},
|
|
||||||
# ETL :{'read':etl.Transporter,'write':etl.Transporter}
|
|
||||||
ETL :{'read':etl.instance,'write':etl.instance}
|
|
||||||
}
|
|
||||||
DEFAULT = {PG:{'host':'localhost','port':5432},MYSQL:{'host':'localhost','port':3306}}
|
|
||||||
DEFAULT[MONGODB] = {'port':27017,'host':'localhost'}
|
|
||||||
DEFAULT[REDSHIFT] = DEFAULT[PG]
|
|
||||||
DEFAULT[MARIADB] = DEFAULT[MYSQL]
|
|
||||||
DEFAULT[NETEZZA] = {'port':5480}
|
|
||||||
|
|
@ -0,0 +1,44 @@
|
||||||
|
"""
|
||||||
|
This file is intended to aggregate all we can about the framework in terms of support
|
||||||
|
"""
|
||||||
|
|
||||||
|
BIGQUERY='bigquery'
|
||||||
|
|
||||||
|
POSTGRESQL = 'postgresql'
|
||||||
|
MONGODB = 'mongodb'
|
||||||
|
HTTP='http'
|
||||||
|
BIGQUERY ='bigquery'
|
||||||
|
FILE = 'file'
|
||||||
|
ETL = 'etl'
|
||||||
|
SQLITE = 'sqlite'
|
||||||
|
SQLITE3= 'sqlite3'
|
||||||
|
REDSHIFT = 'redshift'
|
||||||
|
NETEZZA = 'netezza'
|
||||||
|
MYSQL = 'mysql'
|
||||||
|
MARIADB= MYSQL
|
||||||
|
|
||||||
|
COUCHDB = 'couchdb'
|
||||||
|
CONSOLE = 'console'
|
||||||
|
ETL = 'etl'
|
||||||
|
TRANSPORT = ETL
|
||||||
|
NEXTCLOUD = 'nextcloud'
|
||||||
|
S3 = 's3'
|
||||||
|
CALLBACK = 'callback'
|
||||||
|
CONSOLE = 'console'
|
||||||
|
RABBITMQ = 'rabbitmq'
|
||||||
|
DATABRICKS= 'databricks'
|
||||||
|
|
||||||
|
#
|
||||||
|
# synonyms of the above
|
||||||
|
BQ = BIGQUERY
|
||||||
|
MONGO = MONGODB
|
||||||
|
FERRETDB= MONGODB
|
||||||
|
PG = POSTGRESQL
|
||||||
|
PSQL = POSTGRESQL
|
||||||
|
PGSQL = POSTGRESQL
|
||||||
|
|
||||||
|
AWS_S3 = 's3'
|
||||||
|
RABBIT = RABBITMQ
|
||||||
|
|
||||||
|
# QLISTENER = 'qlistener'
|
||||||
|
|
||||||
526
transport/sql.py
526
transport/sql.py
|
|
@ -1,526 +0,0 @@
|
||||||
"""
|
|
||||||
This file is intended to perform read/writes against an SQL database such as PostgreSQL, Redshift, Mysql, MsSQL ...
|
|
||||||
|
|
||||||
LICENSE (MIT)
|
|
||||||
Copyright 2016-2020, The Phi Technology LLC
|
|
||||||
|
|
||||||
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
|
|
||||||
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
|
|
||||||
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
|
||||||
|
|
||||||
|
|
||||||
@TODO:
|
|
||||||
- Migrate SQLite to SQL hierarchy
|
|
||||||
- Include Write in Chunks from pandas
|
|
||||||
"""
|
|
||||||
import psycopg2 as pg
|
|
||||||
import mysql.connector as my
|
|
||||||
import sys
|
|
||||||
|
|
||||||
import sqlalchemy
|
|
||||||
if sys.version_info[0] > 2 :
|
|
||||||
from transport.common import Reader, Writer #, factory
|
|
||||||
else:
|
|
||||||
from common import Reader,Writer
|
|
||||||
import json
|
|
||||||
from google.oauth2 import service_account
|
|
||||||
from google.cloud import bigquery as bq
|
|
||||||
# import constants.bq_utils as bq_consts
|
|
||||||
|
|
||||||
from multiprocessing import Lock, RLock
|
|
||||||
import pandas as pd
|
|
||||||
import pandas_gbq as pd_gbq
|
|
||||||
import numpy as np
|
|
||||||
import nzpy as nz #--- netezza drivers
|
|
||||||
import sqlite3
|
|
||||||
import copy
|
|
||||||
import os
|
|
||||||
import time
|
|
||||||
|
|
||||||
class SQLRW :
|
|
||||||
lock = RLock()
|
|
||||||
MAX_CHUNK = 2000000
|
|
||||||
DRIVERS = {"postgresql":pg,"redshift":pg,"mysql":my,"mariadb":my,"netezza":nz}
|
|
||||||
REFERENCE = {
|
|
||||||
"netezza":{"port":5480,"handler":nz,"dtype":"VARCHAR(512)"},
|
|
||||||
"postgresql":{"port":5432,"handler":pg,"dtype":"VARCHAR"},
|
|
||||||
"redshift":{"port":5432,"handler":pg,"dtype":"VARCHAR"},
|
|
||||||
"mysql":{"port":3360,"handler":my,"dtype":"VARCHAR(256)"},
|
|
||||||
"mariadb":{"port":3360,"handler":my,"dtype":"VARCHAR(256)"},
|
|
||||||
}
|
|
||||||
def __init__(self,**_args):
|
|
||||||
|
|
||||||
|
|
||||||
_info = {}
|
|
||||||
_info['dbname'] = _args['db'] if 'db' in _args else _args['database']
|
|
||||||
self.table = _args['table'] if 'table' in _args else None
|
|
||||||
self.fields = _args['fields'] if 'fields' in _args else []
|
|
||||||
self.schema = _args['schema'] if 'schema' in _args else ''
|
|
||||||
self._chunks = 1 if 'chunks' not in _args else int(_args['chunks'])
|
|
||||||
|
|
||||||
self._provider = _args['provider'] if 'provider' in _args else None
|
|
||||||
# _info['host'] = 'localhost' if 'host' not in _args else _args['host']
|
|
||||||
# _info['port'] = SQLWriter.REFERENCE[_provider]['port'] if 'port' not in _args else _args['port']
|
|
||||||
|
|
||||||
_info['host'] = _args['host'] if 'host' in _args else ''
|
|
||||||
_info['port'] = _args['port'] if 'port' in _args else ''
|
|
||||||
|
|
||||||
# if 'host' in _args :
|
|
||||||
# _info['host'] = 'localhost' if 'host' not in _args else _args['host']
|
|
||||||
# # _info['port'] = SQLWriter.PROVIDERS[_args['provider']] if 'port' not in _args else _args['port']
|
|
||||||
# _info['port'] = SQLWriter.REFERENCE[_provider]['port'] if 'port' not in _args else _args['port']
|
|
||||||
self.lock = False if 'lock' not in _args else _args['lock']
|
|
||||||
if 'username' in _args or 'user' in _args:
|
|
||||||
key = 'username' if 'username' in _args else 'user'
|
|
||||||
_info['user'] = _args[key]
|
|
||||||
_info['password'] = _args['password'] if 'password' in _args else ''
|
|
||||||
if 'auth_file' in _args :
|
|
||||||
_auth = json.loads( open(_args['auth_file']).read() )
|
|
||||||
key = 'username' if 'username' in _auth else 'user'
|
|
||||||
_info['user'] = _auth[key]
|
|
||||||
_info['password'] = _auth['password'] if 'password' in _auth else ''
|
|
||||||
|
|
||||||
_info['host'] = _auth['host'] if 'host' in _auth else _info['host']
|
|
||||||
_info['port'] = _auth['port'] if 'port' in _auth else _info['port']
|
|
||||||
if 'database' in _auth:
|
|
||||||
_info['dbname'] = _auth['database']
|
|
||||||
self.table = _auth['table'] if 'table' in _auth else self.table
|
|
||||||
#
|
|
||||||
# We need to load the drivers here to see what we are dealing with ...
|
|
||||||
|
|
||||||
|
|
||||||
# _handler = SQLWriter.REFERENCE[_provider]['handler']
|
|
||||||
_handler = _args['driver'] #-- handler to the driver
|
|
||||||
self._dtype = _args['default']['type'] if 'default' in _args and 'type' in _args['default'] else 'VARCHAR(256)'
|
|
||||||
# self._provider = _args['provider']
|
|
||||||
# self._dtype = SQLWriter.REFERENCE[_provider]['dtype'] if 'dtype' not in _args else _args['dtype']
|
|
||||||
# self._provider = _provider
|
|
||||||
if _handler == nz :
|
|
||||||
_info['database'] = _info['dbname']
|
|
||||||
_info['securityLevel'] = 0
|
|
||||||
del _info['dbname']
|
|
||||||
if _handler == my :
|
|
||||||
_info['database'] = _info['dbname']
|
|
||||||
del _info['dbname']
|
|
||||||
if _handler == sqlite3 :
|
|
||||||
_info = {'path':_info['dbname'],'isolation_level':'IMMEDIATE'}
|
|
||||||
if _handler != sqlite3 :
|
|
||||||
self.conn = _handler.connect(**_info)
|
|
||||||
else:
|
|
||||||
self.conn = _handler.connect(_info['path'],isolation_level='IMMEDIATE')
|
|
||||||
self._engine = _args['sqlalchemy'] if 'sqlalchemy' in _args else None
|
|
||||||
def meta(self,**_args):
|
|
||||||
schema = []
|
|
||||||
try:
|
|
||||||
if self._engine :
|
|
||||||
table = _args['table'] if 'table' in _args else self.table
|
|
||||||
if sqlalchemy.__version__.startswith('1.') :
|
|
||||||
_m = sqlalchemy.MetaData(bind=self._engine)
|
|
||||||
_m.reflect()
|
|
||||||
else:
|
|
||||||
|
|
||||||
_m = sqlalchemy.MetaData()
|
|
||||||
_m.reflect(bind=self._engine)
|
|
||||||
schema = [{"name":_attr.name,"type":str(_attr.type)} for _attr in _m.tables[table].columns]
|
|
||||||
#
|
|
||||||
# Some house keeping work
|
|
||||||
_m = {'BIGINT':'INTEGER','TEXT':'STRING','DOUBLE_PRECISION':'FLOAT','NUMERIC':'FLOAT','DECIMAL':'FLOAT','REAL':'FLOAT'}
|
|
||||||
for _item in schema :
|
|
||||||
if _item['type'] in _m :
|
|
||||||
_item['type'] = _m[_item['type']]
|
|
||||||
|
|
||||||
except Exception as e:
|
|
||||||
print (e)
|
|
||||||
pass
|
|
||||||
return schema
|
|
||||||
def _tablename(self,name) :
|
|
||||||
|
|
||||||
return self.schema +'.'+name if self.schema not in [None, ''] and '.' not in name else name
|
|
||||||
def has(self,**_args):
|
|
||||||
return self.meta(**_args)
|
|
||||||
# found = False
|
|
||||||
# try:
|
|
||||||
|
|
||||||
# table = self._tablename(_args['table'])if 'table' in _args else self._tablename(self.table)
|
|
||||||
# sql = "SELECT * FROM :table LIMIT 1".replace(":table",table)
|
|
||||||
# if self._engine :
|
|
||||||
# _conn = self._engine.connect()
|
|
||||||
# else:
|
|
||||||
# _conn = self.conn
|
|
||||||
# found = pd.read_sql(sql,_conn).shape[0]
|
|
||||||
# found = True
|
|
||||||
|
|
||||||
# except Exception as e:
|
|
||||||
# print (e)
|
|
||||||
# pass
|
|
||||||
# finally:
|
|
||||||
# if not self._engine :
|
|
||||||
# _conn.close()
|
|
||||||
# return found
|
|
||||||
def isready(self):
|
|
||||||
_sql = "SELECT * FROM :table LIMIT 1".replace(":table",self.table)
|
|
||||||
try:
|
|
||||||
_conn = self.conn if not hasattr(self,'_engine') else self._engine
|
|
||||||
return pd.read_sql(_sql,_conn).columns.tolist()
|
|
||||||
except Exception as e:
|
|
||||||
pass
|
|
||||||
return False
|
|
||||||
def apply(self,_sql):
|
|
||||||
"""
|
|
||||||
This function applies a command and/or a query against the current relational data-store
|
|
||||||
:param _sql insert/select statement
|
|
||||||
@TODO: Store procedure calls
|
|
||||||
"""
|
|
||||||
#
|
|
||||||
_out = None
|
|
||||||
try:
|
|
||||||
if _sql.lower().startswith('select') :
|
|
||||||
|
|
||||||
_conn = self._engine if self._engine else self.conn
|
|
||||||
return pd.read_sql(_sql,_conn)
|
|
||||||
else:
|
|
||||||
# Executing a command i.e no expected return values ...
|
|
||||||
cursor = self.conn.cursor()
|
|
||||||
cursor.execute(_sql)
|
|
||||||
self.conn.commit()
|
|
||||||
except Exception as e :
|
|
||||||
print (e)
|
|
||||||
finally:
|
|
||||||
if not self._engine :
|
|
||||||
self.conn.commit()
|
|
||||||
# cursor.close()
|
|
||||||
def close(self):
|
|
||||||
try:
|
|
||||||
self.conn.close()
|
|
||||||
except Exception as error :
|
|
||||||
print (error)
|
|
||||||
pass
|
|
||||||
class SQLReader(SQLRW,Reader) :
|
|
||||||
def __init__(self,**_args):
|
|
||||||
super().__init__(**_args)
|
|
||||||
|
|
||||||
def read(self,**_args):
|
|
||||||
if 'sql' in _args :
|
|
||||||
_sql = (_args['sql'])
|
|
||||||
else:
|
|
||||||
if 'table' in _args :
|
|
||||||
table = _args['table']
|
|
||||||
else:
|
|
||||||
table = self.table
|
|
||||||
# table = self.table if self.table is not None else _args['table']
|
|
||||||
_sql = "SELECT :fields FROM "+self._tablename(table)
|
|
||||||
if 'filter' in _args :
|
|
||||||
_sql = _sql +" WHERE "+_args['filter']
|
|
||||||
if 'fields' in _args :
|
|
||||||
_fields = _args['fields']
|
|
||||||
else:
|
|
||||||
_fields = '*' if not self.fields else ",".join(self.fields)
|
|
||||||
_sql = _sql.replace(":fields",_fields)
|
|
||||||
#
|
|
||||||
# At this point we have a query we can execute gracefully
|
|
||||||
if 'limit' in _args :
|
|
||||||
_sql = _sql + " LIMIT "+str(_args['limit'])
|
|
||||||
#
|
|
||||||
# @TODO:
|
|
||||||
# It is here that we should inspect to see if there are any pre/post conditions
|
|
||||||
#
|
|
||||||
return self.apply(_sql)
|
|
||||||
def close(self) :
|
|
||||||
try:
|
|
||||||
self.conn.close()
|
|
||||||
except Exception as error :
|
|
||||||
print (error)
|
|
||||||
pass
|
|
||||||
|
|
||||||
class SQLWriter(SQLRW,Writer):
|
|
||||||
def __init__(self,**_args) :
|
|
||||||
super().__init__(**_args)
|
|
||||||
#
|
|
||||||
# In the advent that data typing is difficult to determine we can inspect and perform a default case
|
|
||||||
# This slows down the process but improves reliability of the data
|
|
||||||
# NOTE: Proper data type should be set on the target system if their source is unclear.
|
|
||||||
|
|
||||||
self._cast = False if 'cast' not in _args else _args['cast']
|
|
||||||
|
|
||||||
def init(self,fields=None):
|
|
||||||
# if not fields :
|
|
||||||
# try:
|
|
||||||
# table = self._tablename(self.table)
|
|
||||||
# self.fields = pd.read_sql_query("SELECT * FROM :table LIMIT 1".replace(":table",table),self.conn).columns.tolist()
|
|
||||||
# except Exception as e:
|
|
||||||
# pass
|
|
||||||
# finally:
|
|
||||||
# pass
|
|
||||||
# else:
|
|
||||||
self.fields = fields;
|
|
||||||
|
|
||||||
def make(self,**_args):
|
|
||||||
table = self._tablename(self.table) if 'table' not in _args else self._tablename(_args['table'])
|
|
||||||
if 'fields' in _args :
|
|
||||||
fields = _args['fields']
|
|
||||||
# table = self._tablename(self.table)
|
|
||||||
sql = " ".join(["CREATE TABLE",table," (", ",".join([ name +' '+ self._dtype for name in fields]),")"])
|
|
||||||
|
|
||||||
else:
|
|
||||||
schema = _args['schema'] if 'schema' in _args else []
|
|
||||||
|
|
||||||
_map = _args['map'] if 'map' in _args else {}
|
|
||||||
sql = [] # ["CREATE TABLE ",_args['table'],"("]
|
|
||||||
for _item in schema :
|
|
||||||
_type = _item['type']
|
|
||||||
if _type in _map :
|
|
||||||
_type = _map[_type]
|
|
||||||
sql = sql + [" " .join([_item['name'], ' ',_type])]
|
|
||||||
sql = ",".join(sql)
|
|
||||||
# table = self._tablename(_args['table'])
|
|
||||||
sql = ["CREATE TABLE ",table,"( ",sql," )"]
|
|
||||||
sql = " ".join(sql)
|
|
||||||
|
|
||||||
cursor = self.conn.cursor()
|
|
||||||
try:
|
|
||||||
|
|
||||||
cursor.execute(sql)
|
|
||||||
except Exception as e :
|
|
||||||
print (e)
|
|
||||||
# print (sql)
|
|
||||||
pass
|
|
||||||
finally:
|
|
||||||
# cursor.close()
|
|
||||||
self.conn.commit()
|
|
||||||
pass
|
|
||||||
def write(self,info,**_args):
|
|
||||||
"""
|
|
||||||
:param info writes a list of data to a given set of fields
|
|
||||||
"""
|
|
||||||
# inspect = False if 'inspect' not in _args else _args['inspect']
|
|
||||||
# cast = False if 'cast' not in _args else _args['cast']
|
|
||||||
# if not self.fields :
|
|
||||||
# if type(info) == list :
|
|
||||||
# _fields = info[0].keys()
|
|
||||||
# elif type(info) == dict :
|
|
||||||
# _fields = info.keys()
|
|
||||||
# elif type(info) == pd.DataFrame :
|
|
||||||
# _fields = info.columns.tolist()
|
|
||||||
|
|
||||||
# # _fields = info.keys() if type(info) == dict else info[0].keys()
|
|
||||||
# # _fields = list (_fields)
|
|
||||||
# self.init(_fields)
|
|
||||||
|
|
||||||
try:
|
|
||||||
table = _args['table'] if 'table' in _args else self.table
|
|
||||||
#
|
|
||||||
# In SQL, schema can stand for namespace or the structure of a table
|
|
||||||
# In case we have a list, we are likely dealing with table structure
|
|
||||||
#
|
|
||||||
if 'schema' in _args :
|
|
||||||
if type(_args['schema']) == str :
|
|
||||||
self.schema = _args['schema'] if 'schema' in _args else self.schema
|
|
||||||
elif type(_args['schema']) == list and len(_args['schema']) > 0 and not self.has(table=table):
|
|
||||||
#
|
|
||||||
# There is a messed up case when an empty array is passed (no table should be created)
|
|
||||||
#
|
|
||||||
self.make(table=table,schema=_args['schema'])
|
|
||||||
pass
|
|
||||||
# self.schema = _args['schema'] if 'schema' in _args else self.schema
|
|
||||||
table = self._tablename(table)
|
|
||||||
|
|
||||||
_sql = "INSERT INTO :table (:fields) VALUES (:values)".replace(":table",table) #.replace(":table",self.table).replace(":fields",_fields)
|
|
||||||
|
|
||||||
if type(info) == list :
|
|
||||||
_info = pd.DataFrame(info)
|
|
||||||
elif type(info) == dict :
|
|
||||||
_info = pd.DataFrame([info])
|
|
||||||
else:
|
|
||||||
_info = pd.DataFrame(info)
|
|
||||||
|
|
||||||
|
|
||||||
if _info.shape[0] == 0 :
|
|
||||||
|
|
||||||
return
|
|
||||||
if self.lock :
|
|
||||||
SQLRW.lock.acquire()
|
|
||||||
#
|
|
||||||
# we will adjust the chunks here in case we are not always sure of the
|
|
||||||
if self._chunks == 1 and _info.shape[0] > SQLRW.MAX_CHUNK :
|
|
||||||
self._chunks = 10
|
|
||||||
_indexes = np.array_split(np.arange(_info.shape[0]),self._chunks)
|
|
||||||
for i in _indexes :
|
|
||||||
#
|
|
||||||
# In case we have an invalid chunk ...
|
|
||||||
if _info.iloc[i].shape[0] == 0 :
|
|
||||||
continue
|
|
||||||
#
|
|
||||||
# We are enabling writing by chunks/batches because some persistent layers have quotas or limitations on volume of data
|
|
||||||
|
|
||||||
if self._engine is not None:
|
|
||||||
# pd.to_sql(_info,self._engine)
|
|
||||||
if self.schema in ['',None] :
|
|
||||||
rows = _info.iloc[i].to_sql(table,self._engine,if_exists='append',index=False)
|
|
||||||
else:
|
|
||||||
#
|
|
||||||
# Writing with schema information ...
|
|
||||||
rows = _info.iloc[i].to_sql(self.table,self._engine,schema=self.schema,if_exists='append',index=False)
|
|
||||||
time.sleep(1)
|
|
||||||
else:
|
|
||||||
_fields = ",".join(self.fields)
|
|
||||||
_sql = _sql.replace(":fields",_fields)
|
|
||||||
values = ", ".join("?"*len(self.fields)) if self._provider == 'netezza' else ",".join(["%s" for name in self.fields])
|
|
||||||
_sql = _sql.replace(":values",values)
|
|
||||||
cursor = self.conn.cursor()
|
|
||||||
cursor.executemany(_sql,_info.iloc[i].values.tolist())
|
|
||||||
cursor.close()
|
|
||||||
# cursor.commit()
|
|
||||||
|
|
||||||
# self.conn.commit()
|
|
||||||
except Exception as e:
|
|
||||||
print(e)
|
|
||||||
pass
|
|
||||||
finally:
|
|
||||||
|
|
||||||
if self._engine is None :
|
|
||||||
self.conn.commit()
|
|
||||||
if self.lock :
|
|
||||||
SQLRW.lock.release()
|
|
||||||
# cursor.close()
|
|
||||||
pass
|
|
||||||
def close(self):
|
|
||||||
try:
|
|
||||||
self.conn.close()
|
|
||||||
finally:
|
|
||||||
pass
|
|
||||||
class BigQuery:
|
|
||||||
def __init__(self,**_args):
|
|
||||||
path = _args['service_key'] if 'service_key' in _args else _args['private_key']
|
|
||||||
self.credentials = service_account.Credentials.from_service_account_file(path)
|
|
||||||
self.dataset = _args['dataset'] if 'dataset' in _args else None
|
|
||||||
self.path = path
|
|
||||||
self.dtypes = _args['dtypes'] if 'dtypes' in _args else None
|
|
||||||
self.table = _args['table'] if 'table' in _args else None
|
|
||||||
self.client = bq.Client.from_service_account_json(self.path)
|
|
||||||
def meta(self,**_args):
|
|
||||||
"""
|
|
||||||
This function returns meta data for a given table or query with dataset/table properly formatted
|
|
||||||
:param table name of the name WITHOUT including dataset
|
|
||||||
:param sql sql query to be pulled,
|
|
||||||
"""
|
|
||||||
table = _args['table'] if 'table' in _args else self.table
|
|
||||||
|
|
||||||
try:
|
|
||||||
if table :
|
|
||||||
_dataset = self.dataset if 'dataset' not in _args else _args['dataset']
|
|
||||||
sql = f"""SELECT column_name as name, data_type as type FROM {_dataset}.INFORMATION_SCHEMA.COLUMNS WHERE table_name = '{table}' """
|
|
||||||
_info = {'credentials':self.credentials,'dialect':'standard'}
|
|
||||||
return pd_gbq.read_gbq(sql,**_info).to_dict(orient='records')
|
|
||||||
# return self.read(sql=sql).to_dict(orient='records')
|
|
||||||
# ref = self.client.dataset(self.dataset).table(table)
|
|
||||||
|
|
||||||
# _schema = self.client.get_table(ref).schema
|
|
||||||
# return [{"name":_item.name,"type":_item.field_type,"description":( "" if not hasattr(_item,"description") else _item.description )} for _item in _schema]
|
|
||||||
else :
|
|
||||||
return []
|
|
||||||
except Exception as e:
|
|
||||||
|
|
||||||
return []
|
|
||||||
def has(self,**_args):
|
|
||||||
found = False
|
|
||||||
try:
|
|
||||||
_has = self.meta(**_args)
|
|
||||||
found = _has is not None and len(_has) > 0
|
|
||||||
except Exception as e:
|
|
||||||
pass
|
|
||||||
return found
|
|
||||||
class BQReader(BigQuery,Reader) :
|
|
||||||
def __init__(self,**_args):
|
|
||||||
|
|
||||||
super().__init__(**_args)
|
|
||||||
def apply(self,sql):
|
|
||||||
return self.read(sql=sql)
|
|
||||||
|
|
||||||
def read(self,**_args):
|
|
||||||
SQL = None
|
|
||||||
table = self.table if 'table' not in _args else _args['table']
|
|
||||||
if 'sql' in _args :
|
|
||||||
SQL = _args['sql']
|
|
||||||
elif table:
|
|
||||||
|
|
||||||
table = "".join(["`",table,"`"]) if '.' in table else "".join(["`:dataset.",table,"`"])
|
|
||||||
SQL = "SELECT * FROM :table ".replace(":table",table)
|
|
||||||
if not SQL :
|
|
||||||
return None
|
|
||||||
if SQL and 'limit' in _args:
|
|
||||||
SQL += " LIMIT "+str(_args['limit'])
|
|
||||||
if (':dataset' in SQL or ':DATASET' in SQL) and self.dataset:
|
|
||||||
SQL = SQL.replace(':dataset',self.dataset).replace(':DATASET',self.dataset)
|
|
||||||
_info = {'credentials':self.credentials,'dialect':'standard'}
|
|
||||||
return pd_gbq.read_gbq(SQL,**_info) if SQL else None
|
|
||||||
# return self.client.query(SQL).to_dataframe() if SQL else None
|
|
||||||
|
|
||||||
|
|
||||||
class BQWriter(BigQuery,Writer):
|
|
||||||
lock = Lock()
|
|
||||||
def __init__(self,**_args):
|
|
||||||
super().__init__(**_args)
|
|
||||||
|
|
||||||
self.parallel = False if 'lock' not in _args else _args['lock']
|
|
||||||
self.table = _args['table'] if 'table' in _args else None
|
|
||||||
self.mode = {'if_exists':'append','chunksize':900000,'destination_table':self.table,'credentials':self.credentials}
|
|
||||||
self._chunks = 1 if 'chunks' not in _args else int(_args['chunks'])
|
|
||||||
self._location = 'US' if 'location' not in _args else _args['location']
|
|
||||||
def write(self,_info,**_args) :
|
|
||||||
try:
|
|
||||||
if self.parallel or 'lock' in _args :
|
|
||||||
BQWriter.lock.acquire()
|
|
||||||
_args['table'] = self.table if 'table' not in _args else _args['table']
|
|
||||||
self._write(_info,**_args)
|
|
||||||
finally:
|
|
||||||
if self.parallel:
|
|
||||||
BQWriter.lock.release()
|
|
||||||
def submit(self,_sql):
|
|
||||||
"""
|
|
||||||
Write the output of a massive query to a given table, biquery will handle this as a job
|
|
||||||
This function will return the job identifier
|
|
||||||
"""
|
|
||||||
_config = bq.QueryJobConfig()
|
|
||||||
_config.destination = self.client.dataset(self.dataset).table(self.table)
|
|
||||||
_config.allow_large_results = True
|
|
||||||
# _config.write_disposition = bq.bq_consts.WRITE_APPEND
|
|
||||||
_config.dry_run = False
|
|
||||||
# _config.priority = 'BATCH'
|
|
||||||
_resp = self.client.query(_sql,location=self._location,job_config=_config)
|
|
||||||
return _resp.job_id
|
|
||||||
def status (self,_id):
|
|
||||||
return self.client.get_job(_id,location=self._location)
|
|
||||||
def _write(self,_info,**_args) :
|
|
||||||
_df = None
|
|
||||||
if type(_info) in [list,pd.DataFrame] :
|
|
||||||
if type(_info) == list :
|
|
||||||
_df = pd.DataFrame(_info)
|
|
||||||
elif type(_info) == pd.DataFrame :
|
|
||||||
_df = _info
|
|
||||||
|
|
||||||
if '.' not in _args['table'] :
|
|
||||||
self.mode['destination_table'] = '.'.join([self.dataset,_args['table']])
|
|
||||||
else:
|
|
||||||
|
|
||||||
self.mode['destination_table'] = _args['table'].strip()
|
|
||||||
if 'schema' in _args :
|
|
||||||
self.mode['table_schema'] = _args['schema']
|
|
||||||
#
|
|
||||||
# Let us insure that the types are somewhat compatible ...
|
|
||||||
# _map = {'INTEGER':np.int64,'DATETIME':'datetime64[ns]','TIMESTAMP':'datetime64[ns]','FLOAT':np.float64,'DOUBLE':np.float64,'STRING':str}
|
|
||||||
# _mode = copy.deepcopy(self.mode)
|
|
||||||
_mode = self.mode
|
|
||||||
# _df.to_gbq(**self.mode) #if_exists='append',destination_table=partial,credentials=credentials,chunksize=90000)
|
|
||||||
#
|
|
||||||
# Let us adjust the chunking here
|
|
||||||
self._chunks = 10 if _df.shape[0] > SQLRW.MAX_CHUNK and self._chunks == 1 else self._chunks
|
|
||||||
_indexes = np.array_split(np.arange(_df.shape[0]),self._chunks)
|
|
||||||
for i in _indexes :
|
|
||||||
_df.iloc[i].to_gbq(**self.mode)
|
|
||||||
time.sleep(1)
|
|
||||||
pass
|
|
||||||
#
|
|
||||||
# Aliasing the big query classes allowing it to be backward compatible
|
|
||||||
#
|
|
||||||
BigQueryReader = BQReader
|
|
||||||
BigQueryWriter = BQWriter
|
|
||||||
|
|
@ -0,0 +1,18 @@
|
||||||
|
"""
|
||||||
|
This namespace/package wrap the sql functionalities for a certain data-stores
|
||||||
|
- netezza, postgresql, mysql and sqlite
|
||||||
|
- mariadb, redshift (also included)
|
||||||
|
"""
|
||||||
|
from . import postgresql, mysql, netezza, sqlite
|
||||||
|
|
||||||
|
|
||||||
|
#
|
||||||
|
# Creating aliases for support of additional data-store providerss
|
||||||
|
#
|
||||||
|
mariadb = mysql
|
||||||
|
redshift = postgresql
|
||||||
|
sqlite3 = sqlite
|
||||||
|
|
||||||
|
|
||||||
|
# from transport import sql
|
||||||
|
|
||||||
|
|
@ -0,0 +1,125 @@
|
||||||
|
"""
|
||||||
|
This file encapsulates common operations associated with SQL databases via SQLAlchemy
|
||||||
|
|
||||||
|
"""
|
||||||
|
import sqlalchemy as sqa
|
||||||
|
import pandas as pd
|
||||||
|
|
||||||
|
class Base:
|
||||||
|
def __init__(self,**_args):
|
||||||
|
self._host = _args['host'] if 'host' in _args else 'localhost'
|
||||||
|
self._port = None
|
||||||
|
self._database = _args['database']
|
||||||
|
self._table = _args['table'] if 'table' in _args else None
|
||||||
|
self._engine= sqa.create_engine(self._get_uri(**_args),future=True)
|
||||||
|
def _set_uri(self,**_args) :
|
||||||
|
"""
|
||||||
|
:provider provider
|
||||||
|
:host host and port
|
||||||
|
:account account user/pwd
|
||||||
|
"""
|
||||||
|
_account = _args['account'] if 'account' in _args else None
|
||||||
|
_host = _args['host']
|
||||||
|
_provider = _args['provider'].replace(':','').replace('/','').strip()
|
||||||
|
def _get_uri(self,**_args):
|
||||||
|
"""
|
||||||
|
This function will return the formatted uri for the sqlAlchemy engine
|
||||||
|
"""
|
||||||
|
raise Exception ("Function Needs to be implemented ")
|
||||||
|
def meta (self,**_args):
|
||||||
|
"""
|
||||||
|
This function returns the schema (table definition) of a given table
|
||||||
|
:table optional name of the table (can be fully qualified)
|
||||||
|
"""
|
||||||
|
_table = self._table if 'table' not in _args else _args['table']
|
||||||
|
_schema = []
|
||||||
|
if _table :
|
||||||
|
if sqa.__version__.startswith('1.') :
|
||||||
|
_handler = sqa.MetaData(bind=self._engine)
|
||||||
|
_handler.reflect()
|
||||||
|
else:
|
||||||
|
#
|
||||||
|
# sqlalchemy's version 2.+
|
||||||
|
_handler = sqa.MetaData()
|
||||||
|
_handler.reflect(bind=self._engine)
|
||||||
|
#
|
||||||
|
# Let us extract the schema with the native types
|
||||||
|
_map = {'BIGINT':'INTEGER','TEXT':'STRING','DOUBLE_PRECISION':'FLOAT','NUMERIC':'FLOAT','DECIMAL':'FLOAT','REAL':'FLOAT'}
|
||||||
|
_schema = [{"name":_attr.name,"type":_map.get(str(_attr.type),str(_attr.type))} for _attr in _handler.tables[_table].columns]
|
||||||
|
return _schema
|
||||||
|
def has(self,**_args):
|
||||||
|
return self.meta(**_args)
|
||||||
|
def apply(self,sql):
|
||||||
|
"""
|
||||||
|
Executing sql statement that returns query results (hence the restriction on sql and/or with)
|
||||||
|
:sql SQL query to be exectued
|
||||||
|
|
||||||
|
@TODO: Execution of stored procedures
|
||||||
|
"""
|
||||||
|
return pd.read_sql(sql,self._engine) if sql.lower().startswith('select') or sql.lower().startswith('with') else None
|
||||||
|
|
||||||
|
class SQLBase(Base):
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
def get_provider(self):
|
||||||
|
raise Exception ("Provider Needs to be set ...")
|
||||||
|
def get_default_port(self) :
|
||||||
|
raise Exception ("default port needs to be set")
|
||||||
|
|
||||||
|
def _get_uri(self,**_args):
|
||||||
|
_host = self._host
|
||||||
|
_account = ''
|
||||||
|
if self._port :
|
||||||
|
_port = self._port
|
||||||
|
else:
|
||||||
|
_port = self.get_default_port()
|
||||||
|
|
||||||
|
_host = f'{_host}:{_port}'
|
||||||
|
|
||||||
|
if 'username' in _args :
|
||||||
|
_account = ''.join([_args['username'],':',_args['password'],'@'])
|
||||||
|
_database = self._database
|
||||||
|
_provider = self.get_provider().replace(':','').replace('/','')
|
||||||
|
# _uri = [f'{_provider}:/',_account,_host,_database]
|
||||||
|
# _uri = [_item.strip() for _item in _uri if _item.strip()]
|
||||||
|
# return '/'.join(_uri)
|
||||||
|
return f'{_provider}://{_host}/{_database}' if _account == '' else f'{_provider}://{_account}{_host}/{_database}'
|
||||||
|
|
||||||
|
class BaseReader(SQLBase):
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
def read(self,**_args):
|
||||||
|
"""
|
||||||
|
This function will read a query or table from the specific database
|
||||||
|
"""
|
||||||
|
if 'sql' in _args :
|
||||||
|
sql = _args['sql']
|
||||||
|
else:
|
||||||
|
_table = _args['table'] if 'table' in _args else self._table
|
||||||
|
sql = f'SELECT * FROM {_table}'
|
||||||
|
return self.apply(sql)
|
||||||
|
|
||||||
|
|
||||||
|
class BaseWriter (SQLBase):
|
||||||
|
"""
|
||||||
|
This class implements SQLAlchemy support for Writting to a data-store (RDBMS)
|
||||||
|
"""
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
def write(self,_data,**_args):
|
||||||
|
if type(_data) == dict :
|
||||||
|
_df = pd.DataFrame(_data)
|
||||||
|
elif type(_data) == list :
|
||||||
|
_df = pd.DataFrame(_data)
|
||||||
|
else:
|
||||||
|
_df = _data.copy()
|
||||||
|
#
|
||||||
|
# We are assuming we have a data-frame at this point
|
||||||
|
#
|
||||||
|
_table = _args['table'] if 'table' in _args else self._table
|
||||||
|
_mode = {'chunksize':2000000,'if_exists':'append','index':False}
|
||||||
|
if 'schema' in _args :
|
||||||
|
_mode['schema'] = _args['schema']
|
||||||
|
if 'if_exists' in _args :
|
||||||
|
_mode['if_exists'] = _args['if_exists']
|
||||||
|
_df.to_sql(_table,self._engine,**_args,index=False)
|
||||||
|
|
@ -0,0 +1,18 @@
|
||||||
|
"""
|
||||||
|
This file implements support for mysql and maria db (with drivers mysql+mysql)
|
||||||
|
"""
|
||||||
|
from transport.sql.common import BaseReader, BaseWriter
|
||||||
|
# import mysql.connector as my
|
||||||
|
class MYSQL:
|
||||||
|
|
||||||
|
def get_provider(self):
|
||||||
|
return "mysql+mysqlconnector"
|
||||||
|
def get_default_port(self):
|
||||||
|
return "3306"
|
||||||
|
class Reader(MYSQL,BaseReader) :
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
|
||||||
|
class Writer(MYSQL,BaseWriter) :
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
|
@ -0,0 +1,15 @@
|
||||||
|
import nzpy as nz
|
||||||
|
from transport.sql.common import BaseReader, BaseWriter
|
||||||
|
|
||||||
|
class Netezza:
|
||||||
|
def get_provider(self):
|
||||||
|
return 'netezza+nzpy'
|
||||||
|
def get_default_port(self):
|
||||||
|
return '5480'
|
||||||
|
|
||||||
|
class Reader(Netezza,BaseReader) :
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
class Writer(Netezza,BaseWriter):
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
|
@ -0,0 +1,22 @@
|
||||||
|
|
||||||
|
from transport.sql.common import BaseReader , BaseWriter
|
||||||
|
from psycopg2.extensions import register_adapter, AsIs
|
||||||
|
import numpy as np
|
||||||
|
|
||||||
|
register_adapter(np.int64, AsIs)
|
||||||
|
|
||||||
|
class PG:
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
def get_provider(self):
|
||||||
|
return "postgresql"
|
||||||
|
|
||||||
|
def get_default_port(self):
|
||||||
|
return "5432"
|
||||||
|
class Reader(PG,BaseReader) :
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
class Writer(PG,BaseWriter):
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
|
||||||
|
|
@ -0,0 +1,25 @@
|
||||||
|
import sqlalchemy
|
||||||
|
import pandas as pd
|
||||||
|
from transport.sql.common import Base, BaseReader, BaseWriter
|
||||||
|
class SQLite (BaseReader):
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
if 'path' in _args :
|
||||||
|
self._database = _args['path']
|
||||||
|
if 'database' in _args :
|
||||||
|
self._database = _args['database']
|
||||||
|
def _get_uri(self,**_args):
|
||||||
|
path = self._database
|
||||||
|
return f'sqlite:///{path}' # ensure this is the correct path for the sqlite file.
|
||||||
|
|
||||||
|
class Reader(SQLite,BaseReader):
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
|
# def read(self,**_args):
|
||||||
|
# sql = _args['sql']
|
||||||
|
# return pd.read_sql(sql,self._engine)
|
||||||
|
|
||||||
|
|
||||||
|
class Writer (SQLite,BaseWriter):
|
||||||
|
def __init__(self,**_args):
|
||||||
|
super().__init__(**_args)
|
||||||
Loading…
Reference in New Issue