data-maker/pipeline.py

#!/usr/bin/env python3
import json
from transport import factory
import numpy as np
import time
import os
from multiprocessing import Process, Lock
import pandas as pd
from google.oauth2 import service_account
from google.cloud import bigquery as bq
import data.maker
import copy
from data.params import SYS_ARGS 

#
# The configuration array is now loaded and we will execute the pipe line as follows

class Components :
	lock = Lock()
	class KEYS :
		PIPELINE_KEY = 'pipeline'
		SQL_FILTER = 'filter'
	@staticmethod
	def get_filter (**args):
		if args['qualifier'] == 'IN' :
			return ' '.join([args['field'],args['qualifier'],'(',args['value'],')'])
		else:
			return ' '.join([args['field'],args['qualifier'],args['value']])
	@staticmethod
	def get_logger(**args) :
		return factory.instance(type='mongo.MongoWriter',args={'dbname':'aou','doc':args['context']})
	@staticmethod
	def get(args):
		"""
		This function returns a data-frame provided a bigquery sql statement with conditions (and limits for testing purposes)
		The function must be wrapped around a lambda this makes testing easier and changing data stores transparent to the rest of the code. (Vital when testing)
		:sql	basic sql statement
		:condition	optional condition and filters
		"""
		SQL = args['sql']
		if Components.KEYS.SQL_FILTER in args :
			FILTER_KEY = Components.KEYS.SQL_FILTER
			SQL_FILTER = args[FILTER_KEY] if type(args[FILTER_KEY]) == list else [args[FILTER_KEY]]
			# condition = ' '.join([args[FILTER_KEY]['field'],args[FILTER_KEY]['qualifier'],'(',args[FILTER_KEY]['value'],')'])
			
			condition = ' AND '.join([Components.get_filter(**item) for item in SQL_FILTER])
			SQL = " ".join([SQL,'WHERE',condition])

		SQL = SQL.replace(':dataset',args['dataset']) #+ " LI "
		
		if 'limit' in args :
			SQL = SQL + ' LIMIT ' + args['limit']
		#
		# let's log the sql query that has been performed here
		logger = factory.instance(type='mongo.MongoWriter',args={'dbname':'aou','doc':args['context']})
		logger.write({"module":"bigquery","action":"read","input":{"sql":SQL}})
		credentials = service_account.Credentials.from_service_account_file('/home/steve/dev/aou/accounts/curation-prod.json')
		df = pd.read_gbq(SQL,credentials=credentials,dialect='standard')
		return df
		
		# return lambda: pd.read_gbq(SQL,credentials=credentials,dialect='standard')[args['columns']].dropna()
	@staticmethod
	def split(X,MAX_ROWS=3,PART_SIZE=3):
		
		return list(pd.cut( np.arange(X.shape[0]+1),PART_SIZE).categories)

	def train(self,**args):
		"""
		This function will perform training on the basis of a given pointer that reads data

		"""
		schema = None
		if 'file' in args :
			
			df = pd.read_csv(args['file'])
			del args['file']
		elif 'data' not in args :
			reader = factory.instance(**args['store']['source'])
			if 'row_limit' in args :
				df = reader.read(sql=args['sql'],limit=args['row_limit'])
			else:
				df = reader.read(sql=args['sql'])
			schema = reader.meta(table=args['from']) if hasattr(reader,'meta') and 'from' in args else None
		else:
			df = args['data']
			
			
		# df = df.fillna('')
		if schema :
			_schema = {}
			for _item in schema :                
				_type = int
				_value = 0
				if _item.field_type == 'FLOAT' :
					_type =float
				elif _item.field_type != 'INTEGER' :
					_type = str
					_value = ''
				_schema[_item.name] = _type
				df[_item.name] = df[_item.name].fillna(_value).astype(_type)
			args['schema'] = _schema
		# 		df[_item.name] = df[_item.name].astype(_type)
		_args = copy.deepcopy(args)
		# _args['store']  = args['store']['source']
		_args['data'] = df
		
		data.maker.train(**_args)
		
		if 'autopilot' in ( list(args.keys())) :
			print (['autopilot mode enabled ....',args['context']])
			self.generate(args)

		pass

	def post(self,args):
		pass
			

	# @staticmethod
	def generate(self,args):
		"""
		This function will generate data and store it to a given,
		"""
		store = args['store']['logs']
		store['doc'] = args['context']
		logger = factory.instance(**store) #type='mongo.MongoWriter',args={'dbname':'aou','doc':args['context']})

		ostore = args['store']['target']
		writer = factory.instance(**ostore)
		# log_folder = args['logs'] if 'logs' in args else 'logs'
		# partition = args['partition'] if 'partition' in args else ''
		# log_folder = os.sep.join([log_folder,args['context'],str(partition)])
		
		# _args = {"batch_size":2000,"logs":log_folder,"context":args['context'],"max_epochs":150,"column":args['columns'],"id":"person_id","logger":logger}
		# _args['max_epochs'] = 150 if 'max_epochs' not in args else int(args['max_epochs'])
		# _args['num_gpu'] = int(args['num_gpu']) if 'num_gpu' in args else 1 
		# if 'batch_size' in args :
		# 	_args['batch_size'] = int(args['batch_size'])
		
		# if int(args['num_gpu']) > 1 :
		# 	_args['gpu'] = int(args['gpu']) if int(args['gpu']) < 8 else np.random.choice(np.arange(8)).astype(int)
		# else:
		# 	_args['gpu']  = 0
		# _args['num_gpu'] 	= 1
		# os.environ['CUDA_VISIBLE_DEVICES'] = str(args['gpu']) 
		# # _args['no_value']= args['no_value']
		# _args['matrix_size'] = args['matrix_size'] if 'matrix_size' in args else 128
			
		
		# # MAX_ROWS = args['max_rows']  	if 'max_rows' in args else 0
		# PART_SIZE = int(args['part_size']) if 'part_size' in args else 8
		
		# credentials = service_account.Credentials.from_service_account_file('/home/steve/dev/aou/accounts/curation-prod.json')
		# _args['data'] = pd.read_gbq(SQL,credentials=credentials,dialect='standard').dropna()
		# reader = args['reader']
		# df = reader()
		schema = args['schema'] if 'schema' in args else None
		if 'file' in args :
			
			df = pd.read_csv(args['file'])
		else:
			if 'data' not in args :
				reader = factory.instance(**args['store']['source'])
				if 'row_limit' in args :
					df = reader.read(sql=args['sql'],limit=args['row_limit'])
				else:
					df = reader.read(sql=args['sql'])
				if 'schema' not in args and hasattr(reader,'meta'):
					schema = reader.meta(table=args['from'])

					
			else:
				#
				# This will account for autopilot mode ...
				df = args['data']
	
		_info = {"module":"gan-prep","action":"read","shape":{"rows":df.shape[0],"columns":df.shape[0]}}
		
				
		_dc = pd.DataFrame()
		# for mdf in df :
		args['data'] = df
		args['candidates']	= 1 if 'candidates' not in args else int(args['candidates'])
		
		candidates = (data.maker.generate(**args))
		if 'sql.BQWriter' in ostore['type'] :
			#table = ".".join([ostore['['dataset'],args['context']])
			# writer  = factory.instance(**ostore)
			_columns = None
			skip_columns = []
			_schema = [{"name":field.name,"type":field.field_type,"description":field.description} for field in schema] if schema else []
			for _df in candidates :
				#
				# we need to format the fields here to make sure we have something cohesive
				#

				if not skip_columns :
					# _columns = set(df.columns) - set(_df.columns)
					if 'ignore' in args and 'columns' in args['ignore'] :
							
							for name in args['ignore']['columns'] :
								for _name in _df.columns:
									if _name in name:
										skip_columns.append(_name)
				#
				# We perform a series of set operations to insure that the following conditions are met:
				#	- the synthetic dataset only has fields that need to be synthesized
				#	- The original dataset has all the fields except those that need to be synthesized
				#
				
				_df = _df[list(set(_df.columns)  - set(skip_columns))]
				
				if set(df.columns) & set(_df.columns) :
					_columns = set(df.columns) - set(_df.columns)
					df = df[_columns]

				#
				# Let us merge the dataset here and and have a comprehensive dataset

				_df = pd.DataFrame.join(df,_df)
				
				writer.write(_df,schema=_schema,table=args['from'])
			# 	writer.write(df,table=table)
			pass
		else:
			pass

		
		# #
		# # We need to post the generate the data in order to :
		# #	1. compare immediately
		# #	2. synthetic copy
		# #
		
		# cols = _dc.columns.tolist()
		
		# data_comp = _args['data'][args['columns']].join(_dc[args['columns']],rsuffix='_io')				#-- will be used for comparison (store this in big query)
		# #
		# # performing basic analytics on the synthetic data generated (easy to quickly asses)
		# #
		# info = {"module":"generate","action":"io.metrics","input":{"rows":data_comp.shape[0],"partition":partition,"logs":[]}}
		
		# #
		# # @TODO: Send data over to a process for analytics
		
		# base_cols = list(set(_args['data'].columns) - set(args['columns']))	#-- rebuilt the dataset (and store it)
		# cols = _dc.columns.tolist()
		# for name in cols :
		# 	_args['data'][name] = _dc[name]

		# #
		# #-- Let us store all of this into bigquery
		# prefix = args['notify']+'.'+_args['context']
		# partition = str(partition)
		# table = '_'.join([prefix,partition,'io']).replace('__','_')
		# folder = os.sep.join([args['logs'],args['context'],partition,'output']) 
		# if 'file' in args :
			
		# 	_fname = os.sep.join([folder,table.replace('_io','_full_io.csv')])
		# 	_pname = os.sep.join([folder,table])+'.csv'
		# 	data_comp.to_csv( _pname,index=False)
		# 	_args['data'].to_csv(_fname,index=False)
			
		# 	_id = 'path'
		# else:

		# 	credentials = service_account.Credentials.from_service_account_file('/home/steve/dev/aou/accounts/curation-prod.json')
		# 	_pname = os.sep.join([folder,table+'.csv'])
		# 	_fname = table.replace('_io','_full_io')
		# 	partial = '.'.join(['io',args['context']+'_partial_io'])
		# 	complete= '.'.join(['io',args['context']+'_full_io'])
		# 	data_comp.to_csv(_pname,index=False)
		# 	if 'dump' in args :
		# 		print (_args['data'].head())
		# 	else:
		# 		Components.lock.acquire()
		# 		data_comp.to_gbq(if_exists='append',destination_table=partial,credentials=credentials,chunksize=90000)	
		# 		_args['data'].to_gbq(if_exists='append',destination_table=complete,credentials=credentials,chunksize=90000)
		# 		Components.lock.release()
		# 	_id = 'dataset'
		# info = {"full":{_id:_fname,"rows":_args['data'].shape[0]},"partial":{"path":_pname,"rows":data_comp.shape[0]} }
		# if partition :
		# 	info ['partition'] = int(partition)
		# logger.write({"module":"generate","action":"write","input":info} )
		
	
	
if __name__ == '__main__' :
	filename = SYS_ARGS['config'] if 'config' in SYS_ARGS else 'config.json'
	f = open (filename)
	_config = json.loads(f.read())
	f.close()	
	PIPELINE = _config['pipeline']
	index = SYS_ARGS['index']
	if index.isnumeric() :
		index = int(SYS_ARGS['index']) 
	else:
		#
		# The index provided is a key to a pipeline entry mainly the context
		#
		N = len(PIPELINE)
		f = [i for i in range(0,N) if PIPELINE[i]['context'] == index]
		index = f[0] if f else 0
	#
	
	print ("..::: ",PIPELINE[index]['context'])
	args =  (PIPELINE[index])
	for key in _config :
		if key == 'pipeline' or key in args:
			#
			# skip in case of pipeline or if key exists in the selected pipeline (provided by index)
			# 
			continue
		args[key] = _config[key]
	
	args = dict(args,**SYS_ARGS)
	if 'matrix_size' in args :
		args['matrix_size'] = int(args['matrix_size'])
	if 'batch_size' not in args :
		args['batch_size']	= 2000 #if 'batch_size' not in args else int(args['batch_size'])
	if 'dataset' not in args :
		args['dataset'] = 'combined20191004v2_deid'
	PART_SIZE = int(args['part_size']) if 'part_size' in args else 8
	#
	# @TODO:
	#	Log what was initiated so we have context of this processing ...
	#
	# if 'listen' not in SYS_ARGS :
	# if 'file' in args :
	# 	DATA = pd.read_csv(args['file']) ;
	# 	schema = []
	# else:
	# 	DATA = Components().get(args)
	# 	client      = bq.Client.from_service_account_json(args["private_key"])
	# 	schema = client.get_table(client.dataset(args['dataset']).table(args['from'])).schema

	# COLUMNS = DATA.columns
	# DATA = np.array_split(DATA,PART_SIZE)
	# args['schema'] = schema
	if 'generate' in SYS_ARGS :
		#
		# Let us see if we have partitions given the log folder
		
		content = os.listdir( os.sep.join([args['logs'],'train',args['context']]))
		generator = Components()
		
		# if ''.join(content).isnumeric() :
		# 	#
		# 	# we have partitions we are working with
			
		# 	jobs = []
			
		# 	# columns = DATA.columns.tolist()
			
		# 	# DATA  = np.array_split(DATA,PART_SIZE)

		# 	for index in range(0,PART_SIZE) :
		# 		if 'focus' in args and int(args['focus']) != index :
		# 			#
		# 			# This handles failures/recoveries for whatever reason
		# 			# If we are only interested in generating data for a given partition 
		# 			continue
		# 		# index = id.index(id)
				
		# 		args['partition'] = index
		# 		args['data'] = DATA[index]
		# 		if int(args['num_gpu']) > 1 :
		# 			args['gpu'] = index
		# 		else:
		# 			args['gpu']=0

		# 		make = lambda _args: (Components()).generate(_args)
		# 		job = Process(target=make,args=(args,))
		# 		job.name = 'generator # '+str(index)
		# 		job.start()
		# 		jobs.append(job)
		# 		# if len(jobs) == 1 :
		# 		# 	job.join()

		# 	print (["Started ",len(jobs),"generators" if len(jobs)>1 else "generator" ])
		# 	while len(jobs)> 0 :
		# 		jobs = [job for job in jobs if job.is_alive()]
		# 		time.sleep(2)
				
		# 		# generator.generate(args)
		# else:
		# 	generator.generate(args)
		# Components.generate(args)
		generator.generate(args)
	
	else:
		
		# DATA  = np.array_split(DATA,PART_SIZE)
		agent = Components()
		agent.train(**args)
		# jobs = []
		# for index in range(0,PART_SIZE) :
		# 	if 'focus' in args and int(args['focus']) != index :
		# 		continue
		# 	args['part_size'] = PART_SIZE
		# 	args['partition'] = index
		# 	args['data'] = DATA[index]
		# 	if int(args['num_gpu']) > 1 :
		# 		args['gpu'] = index
		# 	else:
		# 		args['gpu']=0

		# 	make = lambda _args: (Components()).train(**_args)
		# 	job = Process(target=make,args=( dict(args),))
		# 	job.name = 'Trainer # ' + str(index)
		# 	job.start()
		# 	jobs.append(job)
		# 	# args['gpu']
		# print (["Started ",len(jobs),"trainers" if len(jobs)>1 else "trainer" ])
		# while len(jobs)> 0 :
		# 	jobs = [job for job in jobs if job.is_alive()]
		# 	time.sleep(2)

		# trainer = Components()
		# trainer.train(**args)
		
		
		# Components.train(**args)
#for args in PIPELINE :
	#args['dataset'] = 'combined20190510'
	#process = Process(target=Components.train,args=(args,))
	#process.name = args['context']
	#process.start()
#	Components.train(args)