Steve Nyemba
3 years ago
parent
964ddb06ab
commit
0384a2e96f
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#!/usr/bin/env python3
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"""
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This file will perform basic tasks to finalize the GAN process by performing the following :
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- basic stats & analytics
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- rebuild io to another dataset
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"""
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import pandas as pd
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import numpy as np
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from multiprocessing import Process, Lock
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from google.oauth2 import service_account
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from google.cloud import bigquery as bq
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import transport
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from data.params import SYS_ARGS
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import json
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class Analytics :
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"""
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This class will compile basic analytics about a given dataset i.e compare original/synthetic
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"""
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@staticmethod
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def distribution(**args):
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context = args['context']
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df = args['data']
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#
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#-- This data frame counts unique values for each feature (space)
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df_counts = pd.DataFrame(df.apply(lambda col: col.unique().size),columns=['counts']).T # unique counts
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#
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#-- Get the distributions for common values
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#
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names = [name for name in df_counts.columns.tolist() if name.endswith('_io') == False]
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ddf = df.apply(lambda col: pd.DataFrame(col.values,columns=[col.name]).groupby([col.name]).size() ).fillna(0)
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ddf[context] = ddf.index
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pass
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def distance(**args):
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"""
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This function will measure the distance between
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"""
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pass
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class Utils :
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@staticmethod
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def log(**args):
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logger = transport.factory.instance(type="mongo.MongoWriter",args={"dbname":"aou","doc":"logs"})
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logger.write(args)
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logger.close()
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class get :
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@staticmethod
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def pipeline(table,path) :
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# contexts = args['contexts'].split(',') if type(args['contexts']) == str else args['contexts']
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config = json.loads((open(path)).read())
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pipeline = config['pipeline']
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# return [ item for item in pipeline if item['context'] in contexts]
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pipeline = [item for item in pipeline if 'from' in item and item['from'].strip() == table]
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Utils.log(module=table,action='init',input={"pipeline":pipeline})
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return pipeline
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@staticmethod
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def sql(**args) :
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"""
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This function is intended to build SQL query for the remainder of the table that was not synthesized
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:config configuration entries
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:from source of the table name
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:dataset name of the source dataset
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"""
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SQL = ["SELECT * FROM :from "]
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SQL_FILTER = []
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NO_FILTERS_FOUND = True
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# pipeline = Utils.get.config(**args)
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pipeline = args['pipeline']
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REVERSE_QUALIFIER = {'IN':'NOT IN','NOT IN':'IN','=':'<>','<>':'='}
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for item in pipeline :
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if 'filter' in item :
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if NO_FILTERS_FOUND :
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NO_FILTERS_FOUND = False
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SQL += ['WHERE']
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#
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# Let us load the filter in the SQL Query
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FILTER = item['filter']
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QUALIFIER = REVERSE_QUALIFIER[FILTER['qualifier'].upper()]
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SQL_FILTER += [" ".join([FILTER['field'], QUALIFIER,'(',FILTER['value'],')']).replace(":dataset",args['dataset'])]
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src = ".".join([args['dataset'],args['from']])
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SQL += [" AND ".join(SQL_FILTER)]
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#
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# let's pull the field schemas out of the table definition
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#
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Utils.log(module=args['from'],action='sql',input={"sql":" ".join(SQL) })
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return " ".join(SQL).replace(":from",src)
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def mk(**args) :
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dataset = args['dataset']
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client = args['client'] if 'client' in args else bq.Client.from_service_account_file(args['private_key'])
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#
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# let us see if we have a dataset handy here
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#
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datasets = list(client.list_datasets())
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found = [item for item in datasets if item.dataset_id == dataset]
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if not found :
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return client.create_dataset(dataset)
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return found[0]
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def move (args):
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"""
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This function will move a table from the synthetic dataset into a designated location
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This is the simplest case for finalizing a synthetic data set
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:private_key
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"""
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pipeline = Utils.get.pipeline(args['from'],args['config'])
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_args = json.loads((open(args['config'])).read())
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_args['pipeline'] = pipeline
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# del _args['pipeline']
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args = dict(args,**_args)
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# del args['pipeline']
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# private_key = args['private_key']
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client = bq.Client.from_service_account_json(args['private_key'])
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dataset = args['dataset']
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if pipeline :
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SQL = [ ''.join(["SELECT * FROM io.",item['context'],'_full_io']) for item in pipeline]
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SQL += [Utils.get.sql(**args)]
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SQL = ('\n UNION ALL \n'.join(SQL).replace(':dataset','io'))
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else:
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#
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# moving a table to a designated location
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tablename = args['from']
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if 'sql' not in args :
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SQL = "SELECT * FROM :dataset.:table"
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else:
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SQL = args['sql']
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SQL = SQL.replace(":dataset",dataset).replace(":table",tablename)
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Utils.log(module=args['from'],action='sql',input={'sql':SQL})
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#
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# At this point we have gathered all the tables in the io folder and we should now see if we need to merge with the remainder from the original table
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#
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odataset = mk(dataset=dataset+'_io',client=client)
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# SQL = "SELECT * FROM io.:context_full_io".replace(':context',context)
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config = bq.QueryJobConfig()
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config.destination = client.dataset(odataset.dataset_id).table(args['from'])
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config.use_query_cache = True
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config.allow_large_results = True
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config.priority = 'INTERACTIVE'
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#
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#
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schema = client.get_table(client.dataset(args['dataset']).table(args['from'])).schema
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fields = [" ".join(["CAST (",item.name,"AS",item.field_type.replace("INTEGER","INT64").replace("FLOAT","FLOAT64"),") ",item.name]) for item in schema]
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SQL = SQL.replace("*"," , ".join(fields))
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# print (SQL)
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out = client.query(SQL,location='US',job_config=config)
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Utils.log(module=args['from'],action='move',input={'job':out.job_id})
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return (out.job_id)
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import pandas as pd
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import numpy as np
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from google.oauth2 import service_account
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import json
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# path = '../curation-prod.json'
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# credentials = service_account.Credentials.from_service_account_file(path)
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# df = pd.read_gbq("SELECT * FROM io.icd10_partial_io",credentials=credentials,dialect='standard')
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filename = 'config.json' if 'config' not in SYS_ARGS else SYS_ARGS['config']
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f = open(filename)
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config = json.loads(f.read())
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args = config['pipeline']
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f.close()
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if __name__ == '__main__' :
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"""
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Usage :
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finalize --<move|stats> --contexts <c1,c2,...c3> --from <table>
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"""
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if 'move' in SYS_ARGS :
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if 'init' in SYS_ARGS :
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dep = config['dep'] if 'dep' in config else {}
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info = []
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if 'queries' in dep :
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info += dep['queries']
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print ('________')
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if 'tables' in dep :
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info += dep['tables']
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args = {}
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jobs = []
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for item in info :
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args = {}
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if type(item) == str :
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args['from'] = item
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name = item
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else:
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args = item
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name = item['from']
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args['config'] = SYS_ARGS['config']
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# args['pipeline'] = []
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job = Process(target=move,args=(args,))
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job.name = name
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jobs.append(job)
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job.start()
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# while len(jobs) > 0 :
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# jobs = [job for job in jobs if job.is_alive()]
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# time.sleep(1)
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else:
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move(SYS_ARGS)
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# # table = SYS_ARGS['from']
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# # args = dict(config,**{"private_key":"../curation-prod.json"})
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# args = dict(args,**SYS_ARGS)
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# contexts = [item['context'] for item in config['pipeline'] if item['from'] == SYS_ARGS['from']]
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# log = []
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# if contexts :
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# args['contexts'] = contexts
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# log = move(**args)
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# else:
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# tables = args['from'].split(',')
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# for name in tables :
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# name = name.strip()
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# args['from'] = name
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# log += [move(**args)]
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# print ("\n".join(log))
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else:
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print ("NOT YET READY !")
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