#!/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 format_schema(self,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 return _schema def get_ignore(self,**_args) : if 'columns' in _args and 'data' in _args : _df = _args['data'] terms = _args['columns'] return [name for name in _df.columns if name in terms] return [] 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'] # # if 'ignore' in args and 'columns' in args['ignore'] : _cols = self.get_ignore(data=df,columns=args['ignore']['columns']) df = df[ list(set(df.columns)- set(_cols))] # 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 += [{"name":_item.name,"type":_item.field_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())) : args['data'] = df 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) schema = args['schema'] if 'schema' in args else None if 'data' in args : df = args['data'] else: 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']) schema = [{"name":_item.name,"type":_item.field_type} for _item in schema] # 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 = schema 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'] : skip_columns = self.get_ignore(data=_df,columns=args['ignore']['columns']) # 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)