data-transport/transport/etl.py

#!/usr/bin/env python
__doc__ = """
(c) 2018 - 2021 data-transport
steve@the-phi.com, The Phi Technology LLC
https://dev.the-phi.com/git/steve/data-transport.git

This program performs ETL between 9 supported data sources  : Couchdb, Mongodb, Mysql, Mariadb, PostgreSQL, Netezza,Redshift, Sqlite, File
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.


Usage :
	transport --config <path-to-file.json> --procs <number-procs>
@TODO: Create tables if they don't exist for relational databases
example of configuration :

1. Move data from a folder to a data-store
	transport [--folder <path> ] --config <config.json>	 #-- assuming the configuration doesn't have folder 
	transport --folder <path> --provider <postgresql|mongo|sqlite> --<database|db> <name> --table|doc <document_name>
In this case the configuration should look like :
	{folder:..., target:{}}
2. Move data from one source to another
	transport --config <file.json>
	{source:{..},target:{..}} or [{source:{..},target:{..}},{source:{..},target:{..}}]
	

"""
import pandas as pd
import numpy as np
import json 
import sys
import transport
import time
from multiprocessing import Process
SYS_ARGS = {}
if len(sys.argv) > 1:
    
    N = len(sys.argv)
    for i in range(1,N):
        value = None
        if sys.argv[i].startswith('--'):
            key = sys.argv[i][2:] #.replace('-','')
            SYS_ARGS[key] = 1			
            if i + 1 < N:
                value = sys.argv[i + 1] = sys.argv[i+1].strip()
            if key and value and not value.startswith('--'):
                SYS_ARGS[key] = value
                
        
        i += 2

class Post(Process):
    def __init__(self,**args):
        super().__init__()
        
        if 'provider' not in args['target'] :
            self.PROVIDER = args['target']['type']
            self.writer = 	transport.factory.instance(**args['target'])
        else:
            self.PROVIDER = args['target']['provider']
            args['target']['context'] = 'write'
            self.store = args['target']
            self.store['lock'] = True
            # self.writer = transport.instance(**args['target'])
        #
        # If the table doesn't exists maybe create it ?
        #
        self.rows 	=	 args['rows'].fillna('')
		
    def log(self,**_args) :
        if ETL.logger :
            ETL.logger.info(**_args)
		
    def run(self):
        _info = {"values":self.rows} if 'couch' in self.PROVIDER else self.rows	
        ltypes = self.rows.dtypes.values
        columns = self.rows.dtypes.index.tolist()
        # if not self.writer.has() :

            
            # self.writer.make(fields=columns)
            # ETL.logger.info(module='write',action='make-table',input={"name":self.writer.table})
        self.log(module='write',action='make-table',input={"schema":columns})
        for name in columns :
            if _info[name].dtype in ['int32','int64','int','float','float32','float64'] :
                value = 0
            else:
                value = ''
            _info[name] = _info[name].fillna(value)
        writer = transport.factory.instance(**self.store)
        writer.write(_info)
        writer.close()

		
class ETL (Process):
    logger = None
    def __init__(self,**_args):
        super().__init__()

        self.name 	= _args['id'] if 'id' in _args else 'UNREGISTERED'
        if 'provider' not in _args['source'] :
            #@deprecate
            self.reader = transport.factory.instance(**_args['source'])
        else:
            #
            # This is the new interface
            _args['source']['context'] = 'read'	
            
            self.reader = transport.instance(**_args['source'])
        #
        # do we have an sql query provided or not ....
        # self.sql = _args['source']['sql'] if 'sql' in _args['source'] else None
        self.cmd = _args['source']['cmd'] if 'cmd' in _args['source'] else None
        self._oargs = _args['target'] #transport.factory.instance(**_args['target'])
        self.JOB_COUNT =  _args['jobs']
        self.jobs = []
		# self.logger = transport.factory.instance(**_args['logger'])
    def log(self,**_args) :
        if ETL.logger :
            ETL.logger.info(**_args)
        
    def run(self):
        if self.cmd :
            idf = self.reader.read(**self.cmd)
        else:
            idf = self.reader.read() 
        idf = pd.DataFrame(idf)		
        # idf = idf.replace({np.nan: None}, inplace = True)

        idf.columns = [str(name).replace("b'",'').replace("'","").strip() for name in idf.columns.tolist()]
        self.log(rows=idf.shape[0],cols=idf.shape[1],jobs=self.JOB_COUNT)

        #
        # writing the data to a designated data source 
        #
        try:
            
            
            self.log(module='write',action='partitioning',jobs=self.JOB_COUNT)
            rows = np.array_split(np.arange(0,idf.shape[0]),self.JOB_COUNT)
            
            #
            # @TODO: locks
            for i in np.arange(self.JOB_COUNT) :
                # _id = ' '.join([str(i),' table ',self.name])
                indexes = rows[i]
                segment = idf.loc[indexes,:].copy() #.to_dict(orient='records')
                if segment.shape[0] == 0 :
                    continue
                proc = Post(target = self._oargs,rows = segment,name=str(i))
                self.jobs.append(proc)
                proc.start()
                
                self.log(module='write',action='working',segment=str(self.name),table=self.name,rows=segment.shape[0])
            # while self.jobs :
            # 	jobs = [job for job in proc if job.is_alive()]
            # 	time.sleep(1)
        except Exception as e:
            print (e)
        
    def is_done(self):
        self.jobs = [proc for proc in self.jobs if proc.is_alive()]
        return len(self.jobs) == 0
def instance(**_args):
    """
    :param _info    list of objects with {source,target}`
    :param logger
    """
    logger = _args['logger'] if 'logger' in _args else None
    _info = _args['info']
    if logger and type(logger) != str:
        ETL.logger = logger 
    elif logger == 'console':
        ETL.logger = transport.factory.instance(provider='console',lock=True)
    if type(_info) in [list,dict] :
        _config = _info if type(_info) != dict else [_info]
        #
        # The assumption here is that the objects within the list are {source,target} 
        jobs = []
        for _item in _info :
            
            _item['jobs'] = 5 if 'procs' not in _args else int(_args['procs'])
            _job = ETL(**_item)
            _job.start()
            jobs.append(_job)
        return jobs
        
    else:
        return None

if __name__ == '__main__' :
    _info = json.loads(open (SYS_ARGS['config']).read())
    index = int(SYS_ARGS['index']) if 'index' in SYS_ARGS else None
    procs = []
    for _config in _info :
        if 'source' in SYS_ARGS :
            _config['source'] = {"type":"disk.DiskReader","args":{"path":SYS_ARGS['source'],"delimiter":","}}

        _config['jobs']  = 3 if 'jobs' not in SYS_ARGS else int(SYS_ARGS['jobs'])
        etl = ETL (**_config)
        if index is None:	
            
            etl.start()
            procs.append(etl)

        elif _info.index(_config) == index :
            
            # print (_config)
            procs = [etl]
            etl.start()
            break
    #
    #
    N = len(procs)
    while procs :
        procs = [thread for thread in procs if not thread.is_done()]
        if len(procs) < N :
            print (["Finished ",(N-len(procs)), " remaining ", len(procs)])
            N = len(procs)
        time.sleep(1)
	# print ("We're done !!")